IRS Changing Employee Plans & Exempt Organization Audit Procedures

Employee benefit plans and tax-exempt organizations facing Internal Revenue Service (IRS) audits or investigations after April, 2016, their leaders and advisors should prepare for some changes in the practices IRS agents will use to issue and enforce document requests (IDRs) after March 31.

The IRS  Tax Exempt and Government Entities Division (TEGE) just issued updated internal guidance (Guidance) governing the procedures its agents will use to gather information for employee benefit plan and exempt organization examinations including information requests made in connection with:

  • Employee Benefit Form 5500 Examination Procedures
  • Exempt Organizations Pre-Audit Procedures
  • On-Site Examinations
  • Tax Exempt Bonds Examinations
  • Indian Tribal Government Examinations and
  • Federal, State and Local Governments (FSLG) Examinations

The new Guidance follows other recent announcements of changes of IRS employee plan or exempt organization procedures such as recently announced changes in IRS employee plan correction procedures.  See, e.g., IRS Qualified Plan Correction Procedures Changing 1/1/17.

The new procedures defined in the Guidance apply more broadly and take effect April 1, 2017.  The Guidance also requires that TEGE update the following IRMs to specifically reflect the new procedures within the next two years:

  • IRM 4.71.1, Overview of Form 5500 Examination Procedures;
  • IRM 4.75.10, Exempt Organizations Pre-Audit Procedures;
  • IRM 4.75.11, On-Site Examination Guidelines;
  • IRM 4.81.5, Tax Exempt Bonds Examination Program Procedures – Conducting the Examination;
  • IRM 4.86.5, Conducting Indian Tribal Government Examinations; and
  • IRM 4.90.9, Federal, State and Local Governments (FSLG) – Procedures, Workpapers and Report Writing.

Among other things, the new Guidance will require “active involvement” by managers of IRS examiners’ early in the process.  The Guidance also calls for:

  • Taxpayers to be involved in the IDR process.
  • Examiners to discuss the issue being examined and the information needed with the taxpayer prior to issuing an IDR.
  • Examiners to ensure that the IDR clearly states the issue and the relevant information they are requesting.
  • If the taxpayer does not timely provide the information requested in the IDR by the agreed upon date, including extensions, examiners to issue a delinquency notice.
  • If the taxpayer fails to respond to the delinquency notice or provides an incomplete response, for the examiner to issue a pre-summons notice to advise the taxpayer that the IRS will issue a summons unless the missing items are fully provided.
  • For a summons to be issued if the taxpayer fails to provide a complete response to the pre-summons letter by its response due date.

According to TEGE the new procedures set forth in the Guidance are designed to “ensure” that IRS Counsel is prepared to enforce IDRs through the issuance of a summons when necessary while also reinforcing the IRS’ commitment to the respect of taxpayer rights under the Taxpayer Bill of Rights.  TEGE says the updated procedures established in the Guidance will promote these goals by:

  • Providing for open and meaningful communication between the IRS and taxpayers;
  • Reducing taxpayer burdens
  • Providing for consistent treatment of taxpayers;
  • Allowing the IRS to secure more complete and timely responses to IDRs;
  • Providing consistent timelines for IRS agents to review IDR responses; and
  • Promoting timely issue resolution.

While it remains to be seen exactly how well the new procedures will promote these goals in operation, leaders, sponsors, administrators and tax advisors to employee benefit plans and exempt organizations tagged for audits after the Guidelines take effect will want to ensure that they review and fully understand the new procedures as soon as possible after receiving notice of the audit.

A clear understanding of the procedures can help the entities and their representatives to take advantage of all available options for mitigating exposures and liability from the audit as well as to avoid unfortunate missteps that could result in forfeiture of otherwise available tax-related rights and options or otherwise increase the tax and other associated risks and liabilities of the entities or others associated with them arising from the audit.

Along with responding to these tax-related risks, leaders and advisors of employee benefit plan and exempt organizations also need to keep in mind the often substantial non-tax related risks that may arise concurrently or evolve from a TEGE or other tax-related audit or investigation. The often substantial tax and non-tax exposures typically makes it desirable if not necessary to involve experienced legal counsel in the process as soon as possible.

To help respond to the audit and manage its tax and non-tax related risks and, leaders responsible for these entities generally not only will want to seek legal advice within the scope of attorney-client privilege from legal counsel immediately after receiving an IDR or other notice of an audit or investigation, as well as consider periodically consulting experienced legal counsel for assistance in conducting pre-audit assessment of compliance and other compliance and risk management planning.

Early involvement of legal counsel generally is necessary both to understand and manage both the tax and non-tax exposures associated with the audit, as well as to preserve and utilize the potential benefits of attorney-client privilege and other evidentiary privileges that could help to mitigate both the tax and non-tax related risks.  While federal tax rules afford some evidentiary privileges to certain accounting professionals when providing tax representation or advice, the protective scope of such privileges generally are more limited than attorney-client privilege and work product evidentiary privileges and typically do not apply to non-tax matters. As a result, most entities and their leaders will want to consider involvement of legal counsel to maximize privilege protections and non-tax related exposures even if the parties plan for a qualified tax professional or other consultant to play a significant role in assisting them to prepare for and respond to the audit.

About The Author

Recognized by her peers as a Martindale-Hubble “AV-Preeminent” (Top 1%) and “Top Rated Lawyer” with special recognition LexisNexis® Martindale-Hubbell® as “LEGAL LEADER™ Texas Top Rated Lawyer” in Health Care Law and Labor and Employment Law; as among the “Best Lawyers In Dallas” for her work in the fields of “Labor & Employment,” “Tax: Erisa & Employee Benefits,” “Health Care” and “Business and Commercial Law” by D Magazine, Cynthia Marcotte Stamer is a practicing attorney and management consultant, author, public policy advocate and lecturer widely known for work, teachings and publications.

Ms. Stamer works with health industry and other businesses and their management, employee benefit plans, governments and other organizations deal with all aspects of human resources and workforce, internal controls and regulatory compliance, change management and other performance and operations management and compliance. She supports her clients both on a real-time, “on demand” basis and with longer term basis to deal with daily performance management and operations, emerging crises, strategic planning, process improvement and change management, investigations, defending litigation, audits, investigations or other enforcement challenges, government affairs and public policy.

A Fellow in the American College of Employee Benefit Counsel, the American Bar Foundation and the Texas Bar Foundation, Ms. Stamer also shares her thought leadership, experience and advocacy on these and other concerns by her service in the leadership of a broad range of other professional and civic organization including her involvement as the Vice Chair of the North Texas Healthcare Compliance Association; Executive Director of the Coalition on Responsible Health Policy and its PROJECT COPE: Coalition on Patient Empowerment; former Board President of the early childhood development intervention agency, The Richardson Development Center for Children; former Gulf Coast TEGE Council Exempt Organization Coordinator; a founding Board Member and past President of the Alliance for Healthcare Excellence; former board member and Vice President of the Managed Care Association; past Board Member and Board Compliance Committee Chair for the National Kidney Foundation of North Texas; a member and advisor to the National Physicians’ Council for Healthcare Policy; current Vice Chair of the ABA Tort & Insurance Practice Section Employee Benefits Committee; current Vice Chair of Policy for the Life Sciences Committee of the ABA International Section; Past Chair of the ABA Health Law Section Managed Care & Insurance Section; a current Defined Contribution Plan Committee Co-Chair, former Group Chair and Co-Chair of the ABA RPTE Section Employee Benefits Group; immediate past RPTE Representative to ABA Joint Committee on Employee Benefits Council Representative and current RPTE Representative to the ABA Health Law Coordinating Council; past Chair of the Dallas Bar Association Employee Benefits & Executive Compensation Committee; a former member of the Board of Directors, Treasurer, Member and Continuing Education Chair of the Southwest Benefits Association and others.

Ms. Stamer also is a highly popular lecturer, symposia chair and author, who publishes and speaks extensively on health and managed care industry, human resources, employment, employee benefits, compensation, and other regulatory and operational risk management. Examples of her many highly regarded publications on these matters include the “Texas Payday Law” Chapter of Texas Employment Law, as well as thousands of other publications, programs and workshops these and other concerns for the American Bar Association, ALI-ABA, American Health Lawyers, Society of Human Resources Professionals, the Southwest Benefits Association, the Society of Employee Benefits Administrators, the American Law Institute, Lexis-Nexis, Atlantic Information Services, The Bureau of National Affairs (BNA),, Benefits Magazine, Employee Benefit News, Texas CEO Magazine, HealthLeaders, the HCCA, ISSA, HIMSS, Modern Healthcare, Managed Healthcare, Institute of Internal Auditors, Society of CPAs, Business Insurance, Employee Benefits News, World At Work, Benefits Magazine, the Wall Street Journal, the Dallas Morning News, the Dallas Business Journal, the Houston Business Journal, and many other symposia and publications. She also has served as an Editorial Advisory Board Member for human resources, employee benefit and other management focused publications of BNA,, Employee Benefit News, and many other prominent publications and speaks and conducts training for a broad range of professional organizations and for clients on the Advisory Boards of,, Employee Benefit News, and many other publications. For additional information about Ms. Stamer, see   or contact Ms. Stamer via email here  or via telephone to (469) 767-8872.

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NOTICE: These statements and materials are for general informational and purposes only. They do not establish an attorney-client relationship, are not legal advice, and do not serve as a substitute for legal advice. Readers are urged to engage competent legal counsel for consultation and representation in light of the specific facts and circumstances presented in their unique circumstance at any particular time. No comment or statement in this publication is to be construed as an admission.  The author reserves the right to qualify or retract any of these statements at any time. Likewise, the content is not tailored to any particular situation and does not necessarily address all relevant issues.  Because the law is rapidly evolving and rapidly evolving rules makes it highly likely that subsequent developments could impact the currency and completeness of this discussion. The presenter and the program sponsor disclaim, and have no responsibility to provide any update or otherwise notify any participant of any such change, limitation, or other condition that might affect the suitability of reliance upon these materials or information otherwise conveyed in connection with this program. Readers may not rely upon, are solely responsible for, and assume the risk and all liabilities resulting from their use of this publication.

Circular 230 Compliance. The following disclaimer is included to ensure that we comply with U.S. Treasury Department Regulations. Any statements contained herein are not intended or written by the writer to be used, and nothing contained herein can be used by you or any other person, for the purpose of (1) avoiding penalties that may be imposed under federal tax law, or (2) promoting, marketing or recommending to another party any tax-related transaction or matter addressed herein

©2016 Cynthia Marcotte Stamer. Non-exclusive right to republish granted to Solutions Law Press, Inc.™  All other rights reserved.

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