The Internal Revenue Service (IRS) announced in early November 2025 that it is facing continued payroll tax deposit delays and processing backlogs affecting electronic payments and quarterly tax filings. Employers across the country have reported pending payment statuses and delayed posting for Form 941 submissions, prompting the IRS and Treasury Department to issue official guidance on how to manage federal tax obligations during the disruption.
According to the IRS statement released on June 12, 2025, electronic payments made through the Electronic Federal Tax Payment System (EFTPS) may take longer than usual to post to taxpayer accounts. The agency confirmed that financial institutions are receiving payments, but these remain in pending status until additional verification is completed. These delays have triggered automatic balance-due notices for some businesses, even when the payments were made on time.
IRS officials have advised employers not to call immediately after receiving a notice, emphasizing that the backlog is temporary. If a payment remains unposted after 30 days, employers can contact the agency to verify the transaction. Any penalties or interest added during this period will be removed automatically once payments are correctly recorded.
The EFTPS platform remains the official method for submitting federal tax deposits, including income tax withholding and employment taxes. Employers must initiate payments by 8 p.m. Eastern Time at least one business day before the due date to ensure timely processing. Missing this window—even by a few minutes—can result in late-payment penalties, regardless of available funds in the business bank account.
Employers using payroll services or trusted third parties should confirm that each tax deposit is being initiated correctly under their employer identification number. The IRS recommends checking EFTPS.gov or the IRS Online Account to verify whether deposits have posted before the next payroll period.
As of November 2025, the IRS is still processing paper Form 941 (Employer’s Quarterly Federal Tax Return) submissions received in September. Amended forms not related to Employee Retention Credit claims are being handled from February 2025. Electronic filings, however, continue to process within about 21 days—much faster than paper returns.
In its latest update, the IRS reported that more than 1.1 million paper Form 941 filings are still pending review, with an additional 1.46 million returns suspended due to data discrepancies or errors requiring resolution. These delays impact the timely posting of federal income tax withheld, Social Security, and Medicare taxes, which employers are required to report on a quarterly basis.
The ongoing backlog has caused difficulties for businesses reconciling total taxes owed for each calendar quarter. Employers must still meet all deposit schedules for FICA taxes, Medicare taxes, and the Additional Medicare Tax. Failure to make required federal tax deposits by the due date can result in penalties, even while processing issues persist.
The IRS continues to urge most employers to file electronically and maintain accurate wage and tax statements to ensure employees’ earnings are credited correctly with the Social Security Administration. Filing requirements for Form W-2 and information returns remain unchanged for the 2025 calendar year.
Under current IRS deposit regulations, employers are categorized as either monthly or semiweekly depositors based on their lookback period and total taxes paid. Monthly depositors must make payments by the 15th of the following month, while semiweekly depositors must deposit within three or five business days after payday.
Employers who accumulate $100,000 or more in tax liability on any day must deposit by the next business day. These rules remain in effect even when the IRS experiences posting delays or operational disruptions. The agency reminded taxpayers that a legal holiday extending the due date only applies if both the IRS and the Federal Reserve are closed.
“Employers should continue to make timely deposits through EFTPS, even if payment posting appears delayed,” the IRS said in its November update. “All penalties will be corrected once the transaction is confirmed.”
Tax professionals echoed that advice, stressing that every payment submission should be documented. “Businesses must keep acknowledgment numbers for each EFTPS transaction,” said Angela Carter, a certified tax professional based in Illinois. “These serve as proof of compliance if the IRS system shows a temporary delay or if a payment gets misapplied.”
Employers are responsible for withholding the correct amounts of federal income tax, Social Security tax, and Medicare tax from employees' wages. They must also remit their share of FICA taxes and report both employer and employee contributions each quarter using Form 941. Any adjustments or corrections from previous quarters must be reflected in the next quarter’s filing.
The IRS requires all wage and tax information to be reported on time to prevent penalties and ensure employees receive proper credit for their contributions. Employers who use paper filing methods may experience longer delays in processing, making electronic filing the preferred option.
Employers who use payroll services or third-party processors must still ensure compliance with federal payment and filing requirements. Each business is responsible for confirming that its provider makes timely deposits and files all forms accurately and correctly. The IRS holds the employer—not the payroll service—legally accountable for missed or late deposits.
The IRS has urged employers to remain patient as it works through the backlog. Payments made electronically will eventually post, and the agency will adjust any penalties or interest that resulted from internal delays. Employers should verify all transactions using EFTPS.gov and maintain records of each payment submission.
If a tax deposit remains pending after 30 days, businesses are advised to call the IRS Business and Specialty Tax Line for assistance. In urgent cases—such as an approaching filing deadline or penalty notice—employers can make a same-day wire payment through their financial institution using the Treasury’s same-day taxpayer worksheet.
Tax professionals recommend keeping track of all federal tax deposits and reconciling each transaction at the end of every calendar quarter to ensure all employment tax obligations have been met.
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