Nonprofits that Fail to Timely File Form 990 May Face Steep Penalties

For whatever reason, be it a communication error, a time management issue or just the thought that there are other more important tasks to complete, many nonprofits forget or fail to timely file their Form 990 tax return. This may seem like a simple mistake that will be easily remedied; however, this is not always the case. Penalties for failure to file the Form 990 can be steep – as much as $50,000 for organizations with revenues over $1 million and $10,000 for organizations with revenues below $1 million.

Forms 990 and 990-PF are due the 15th day of the 5th month after the end of the organization’s tax year (May 15 for organizations reporting on a calendar year). Organizations may request two three month extensions to prepare their tax return. However, if the extension requests are not filed or the filing is late, penalties will accrue daily each day the filing is late. This penalty may be charged for either a late filed return, an incomplete return, or both.

Penalties are based on the organization’s gross receipts. If an organization whose gross receipts are less than $1,000,000 for its tax year files its Form 990 after the due date (including any extensions), and the organization doesn’t provide reasonable cause for the late filing, the IRS will impose a penalty of $20 per day for each day the return is late. The maximum penalty is $10,000, or 5 percent of the organization’s gross receipts, whichever is less. For organizations with gross receipts in excess of $1,000,000, the penalty increases to $100 per day, up to a maximum of $50,000.

Fortunately, for nonprofits with reasonable cause for filing late, there is a silver lining. Code Section 6652(c)(3) provides that penalties assessed for late filing may be waived when the late filing was due to “reasonable cause.” Accordingly, the IRS will consider waiving the penalties (but not the interest) where the organization can prove the late filing was due to reasonable cause. The waiver request must be made in the form of a written statement that contains a declaration by an officer or director that the statement is made under penalties of perjury. The statement must set forth all the facts regarding the factors that prevented the organization from timely filing its return including:

  • What prevented the organization from requesting an extension of time to file its return if an extension was not requested;
  • How the organization was not neglectful or careless, but exercised ordinary business care and prudence; and
  • What steps have been taken to prevent the same situation from occurring in the future?

The statement should be filed as an attachment to the 990 and should include appropriate documentation. Alternatively, the request can be submitted in response to the penalty notice.

While the IRS does offer abatement in certain cases, organizations should not assume that penalties will be abated. The IRS can be stingy with penalty abatement requests, particularly if its not the organization’s first offense. The best way for a nonprofit to avoid IRS penalties is to be aware of when its tax return is due and take care to ensure an extension is requested or the return is filed by the deadline.

Ellis Carter is a nonprofit lawyer licensed to practice in Washington and Arizona. Ellis advises tax-exempt clients on federal tax matters nationwide.

9 Responses to Nonprofits that Fail to Timely File Form 990 May Face Steep Penalties

  1. Hello, I wanted to inform you of Aplos Software. We provide simple and affordable fund accounting software to non profit organizations, and have also just recently developed an IRS approved e-File 990-N tool that is completely FREE. I would love to communicate with someone about getting the word out on this site. Thank you.

  2. Is it correct to say that if an organization has $300,000 in gross revenues and files 90 days late, then the penalty is $1,800 ($20/day * 90 days)?
    Thanks for your help.

  3. Wouldn’t 4 1/2 months be May 15? May 15 is not 5 1/2 months. April is 4 completed months and the 15th of May would be 1/2.

  4. I think you are correct if you are counting days but not when referencing which month the return is due – the IRS agrees with me – see page 6 of the Form 990 instructions.

  5. Form 990 instructions state “the 15th day of the 5th month” not “5 1/2 months after the tax year”. May 15th is the 15th day of the 5th month for calendar year organizations. It is also 4 1/2 months after the year end. So Todd is correct. The author is mistaken!

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