Update on IRS tax-exempt and government entities compliance priorities

September 2024

In brief

What happened?

The Treasury Inspector General for Tax Administration (TIGTA) recently published a report recommending improvements to the IRS Tax-Exempt Compliance Unit (TECU) that could reduce mistakes and unproductive examination referrals. The IRS Tax-Exempt and Government Division (TE/GE) also released its FY24 program letter and updated its compliance program and priorities web page on IRS.gov. In addition, the IRS has undertaken a project to audit tax-exempt hospitals on compliance with Section 501(r) and the community benefit standard.  

Why is it relevant? 

These reports and programs give insight into IRS operations and reflect the agency’s current compliance focus on exempt organization compliance, including employment tax, compensation excise tax, green energy credits, and tax-exempt hospitals. 

Action to consider 

Organizations should be aware of IRS compliance priorities and take steps to be prepared in case of an IRS inquiry. 

In detail

Recommendations from the TIGTA audit of TECU   

TECU’s primary function is to conduct compliance checks to ensure taxpayers meet federal tax return filing obligations. Participation in the compliance checks is voluntary. TECU workstreams include:   

  • Credit Balance Non-Filer: Obtain delinquent employment tax returns from organizations that have made payroll deposits.  
  • Non-Filers of Form 5500–EZ, Annual Return of a One Participant (Owners/Partners and Their Spouses) Retirement Plan of A Foreign Plan: Obtain Forms 5500–EZ for terminated retirement plans.  
  • Affordable Care Act Hospital Review Compliance Checks: Address discrepancies between hospital-filed tax returns, the information on the hospital website, and the requirements under Section 501(r)(4) identified by the Affordable Care Act Hospital Review group.  
  • Non-Filers of Form 940, Employer’s Annual Federal Unemployment (FUTA) Tax Return: Obtain delinquent Forms 940 from organizations that have filed Form 941, Employer’s Quarterly Federal Tax Return, to verify the proper amounts of Federal unemployment tax have been reported.  
  • Section 4960 Excess Compensation Excise Tax: Obtain delinquent excise tax returns for the top five highly compensated employees of a tax-exempt organization.  
  • Form 990–T, Exempt Organization Business Income Tax Return: Obtain delinquent unrelated business income tax returns.  
  • Combined Annual Wage Reporting-Employment Tax: Compares the total employee wages reported by the employer on the Form W-2, Wage and Tax Statement, to the wages reported by the employer on the Form 941.  

TIGTA conducted an audit to assess the effectiveness of TECU’s efforts to improve tax administration of tax-exempt organizations. Among the findings of the TIGTA audit were:  

  • To promote efficiency, TECU examiners within each work group were required to conduct additional research to identify other potential delinquencies, to promote a “single contact with the taxpayer.” However, this led to TECU experiencing several inefficiencies, hindering its effectiveness and creating the opposite effect. Primarily, examiners now were manually searching for delinquencies that could have been systemically identified by other work groups. There are no controls in place to identify circumstances where an organization falls within multiple workstreams and thus is at risk of being contacted by more than one TECU examiner. Further, examiners spent more hours closing cases, and therefore fewer taxpayers were reached. TECU examiners often made mistakes, such as failing to identify all delinquent returns or not posting secured returns to taxpayers' accounts.   
  • Referrals for examination were largely unproductive, with only 5% assigned to the TE/GE Examination function, and most cases closed without changes. TECU also lacks quantifiable performance goals, complicating effectiveness measurement.  

As a result, TIGTA made six recommendations to address identified issues. The recommendations include:  

  1. Developing a workstream for taxpayers with multiple delinquencies;  
  2. Eliminating the additional research requirement;  
  3. Issuing clear compliance check procedural guidance;  
  4. Revising contact letters for electronic submission of tax returns;  
  5. Aligning examination referral guidance with criteria for assigning cases; and  
  6. Establishing performance goals.  

These recommended improvements would aim to reduce mistakes and unproductive examination referrals, enhancing TECU's effectiveness in tax administration. However, the IRS agreed with only four recommendations, disagreeing with the elimination of the additional research requirement and the establishment of performance goals. The IRS stated that the additional research requirement is enforced to reduce taxpayer burden and administrative cost. The IRS further stated that TECU has performance measures in place that allow TE/GE to evaluate program performance and identify needed changes or improvements. 

Compliance program and priorities  

TE/GE has issued its annual program letter for FY24, which lists TE/GE’s priorities and how those align with the objectives of the IRS Strategic Operating Plan.  

Among the priorities listed in the FY24 program letter are to:  

  • Provide education and outreach to help TE/GE stakeholders make complete and accurate elective payment elections for clean energy credits under the Inflation Reduction Act.  
  • Support effective processing and compliance at pre-filing and filing for elective payment elections of clean energy credits.  
  • Support IRS efforts to proactively review and address Employee Retention Credit claims, during the filing process or immediately after return processing.  
  • Collaborate across IRS on highly complex and or emerging issues including, but not limited to, examinations of ESOPs, tax-exempt hospitals, and high income/high wealth individuals.  

TE/GE also updated the compliance program and priorities web page on IRS.gov.  

The following are compliance strategies approved by the TE/GE Compliance Governance Board to identify, prioritize, and allocate resources within the TE/GE filing population, primarily through IRS exams and compliance checks.  

Worker classification: This strategy will review worker classification to ensure taxpayers are not reducing their tax burden by incorrectly treating workers as independent contractors instead of employees.   

Small exempt organizations that sponsor retirement plans: The focus of this strategy is to review retirement plans of small exempt organizations to determine whether the plan investments are properly administered, whether there are any party-in-interest transactions in the plan trust, and whether any participant loans violate Section 72(p).   

Form 990-N filers/gross receipts model: The purpose of this strategy is to determine if an exempt organization was eligible to file Form 990-N where related filings indicate the $50,000 gross receipts threshold was not met.  

Excise tax on excess compensation: This strategy is to review the impact of the Section 4960 excise tax on excess compensation. Section 4960 imposes a 21% excise tax on tax-exempt organizations that pay over $1 million in compensation to any “covered employee.” IRS review of taxpayer data shows there continues to be a high volume of exempt organizations that paid compensation of over $1 million to at least one “covered employee” but did not report the Section 4960 excise tax on Form 4720, Return of Certain Excise Taxes Under Chapters 41 and 42 of the Internal Revenue Code.   

Tax-exempt collectives using name, image and likeness (NIL) agreements with students: The focus of this strategy is to ensure that exempt organizations identified as supporting athletes through the use of their NIL for compensation disclosed their activities in their application for exempt status, and that those activities are in full compliance with the existing legal requirements under Section 501(a).  

Tax-exempt hospitals: The focus of this strategy is on compliance with the Patient Protection and Affordable Care Act. The IRS will verify whether tax-exempt hospitals are complying with their statutory obligations under Section 501(c)(3), including the community benefit standard, and Section 501(r). The treatment stream for this strategy is examinations. 

Audits of tax-exempt hospitals  

Consistent with its focus on tax-exempt hospitals, the IRS has announced plans to conduct 35 examinations of tax-exempt hospitals focusing on community benefit and compliance with Section 501(r). Additional requirements applicable to tax-exempt hospitals were codified in Section 501(r) pursuant to the 2010 Patient Protection and Affordable Care Act. In addition to operating requirements, Section 501(r) also added reporting requirements and an excise tax.  

Facilities required by a US state to be licensed, registered, or similarly recognized as a hospital, and are tax-exempt under Section 501(c), are subject to the provisions of Section 501(r). Section 501(r) requires tax-exempt hospitals to satisfy four broad requirements to maintain their tax exemptions:  

  • Community Health Needs Assessment (CHNA): Section 501(r)(3) requires tax-exempt hospitals to conduct a CHNA at least once every three years and adopt an implementation strategy to address identified community needs.  
  • Financial Assistance Policy (FAP) and Emergency Medical Care Policy: Section 501(r)(4) requires tax-exempt hospitals to establish and widely publicize a written FAP that includes eligibility criteria for financial assistance, a description of the assistance available, and the application process.  
  • Limitations on Charges: Section 501(r)(5) requires tax-exempt hospitals to limit the amounts charged for emergency or other medically necessary care provided to individuals eligible for assistance under the FAP to not more than the amounts generally billed (AGB) to individuals who have insurance.  
  • Billing and Collections Policy: Section 501(r)(6) prohibits tax-exempt hospitals from engaging in extraordinary collection actions (ECA) before making reasonable efforts to determine whether the individual is eligible for assistance under the FAP.  

Failure to satisfy any requirement of Section 501(r) could require disclosure of such failure on the hospital’s Form 990 or loss of tax-exempt status in the most egregious cases. A failure to comply with the CHNA requirements can also result in a $50,000 excise tax. 

Status of IRS audits  

The IRS recently has intensified its efforts to ensure tax-exempt hospitals are in compliance with the requirements of Section 501(r). Audits will include:  

  • Review of the process for conducting the CHNA, the documentation of the findings, and the implementation strategy adopted to address the needs identified.  
  • Examination of the FAP to ensure it meets the requirements and verification that it is effectively communicated to the public.  
  • Review of billing procedures and patient accounts to ensure compliance with the AGB requirement.  
  • Assessment of the hospital’s billing and collection policies to ensure they align with the FAP requirements and review of cases where ECAs were pursued.  

In addition to document review and evaluation of policies, the IRS may send its auditors to hospital sites for observation and interviews.  

Observation: With the recent interest to ensure Section 501(r) compliance, it is recommended that tax-exempt hospitals maintain transparency in their billing practices, ensure consistent application of their FAP, and keep thorough records of compliance efforts and community health initiatives. All required documentation should be complete and up-to-date, and policies should be reviewed regularly and updated as needed. For purposes of potential Section 501(r) audits, hospitals should consider coding patient accounts in such a manner to avoid violating Health Insurance Portability and Accountability Act (HIPAA) when required to disclose billing information. Further, tax-exempt hospitals should consider regularly training their staff on compliance requirements and best practices. Internal audits could help identify and address potential compliance issues prior to an IRS audit. 

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Ed Geils

Ed Geils

Global and US Tax Knowledge Management Leader, PwC US

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