Is Ultratax's calculation of Failure to Pay Penalty Correct when 90% of tax already paid?
I'm working on a client's 1040 that had an extension filed and they've already paid approximately 90% of their 2022 tax liability. There's still around $8,000 in tax that they owe. What's confusing me is that Ultratax is only calculating interest on the underpayment and not adding any late payment penalty - apparently because they already paid in 90% of what they owed. This doesn't sound right to me. I've been digging through IRS publications for hours and can't find any mention of this 90% rule applying to the Failure to Pay Penalty. I've only seen the 90% threshold mentioned in relation to underpayment of estimated taxes, but nothing about it waiving the Failure to Pay Penalty. From what I can tell, the IRS states that the Failure to Pay Penalty should apply to ANY amount paid after the due date regardless of what percentage was already paid. Am I missing something here? Is Ultratax's calculation actually correct or is there a setting I need to adjust?
19 comments


Dylan Evans
The Ultratax calculation is correct in this case. There's often confusion between the Failure to Pay Penalty and the Estimated Tax Penalty because they have similar thresholds but work differently. For the Failure to Pay Penalty on an extended return, if the taxpayer has paid at least 90% of the total tax liability by the original due date (usually April 15th) AND pays the remaining balance by the extended due date, they won't face the Failure to Pay Penalty. They'll only be subject to interest on the unpaid amount. This is different from the Estimated Tax Penalty (Form 2210), which uses similar percentage thresholds but applies to quarterly estimated payments throughout the year. The key question is: was the remaining $8,000 paid by the extended due date (October 15th, 2022)? If yes, then Ultratax is correct in not calculating a Failure to Pay Penalty.
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Sofia Gomez
•Thanks for clarifying! I'm in a similar situation but my client paid about 85% by the original due date and the rest by the extended due date. Would they be subject to the Failure to Pay Penalty on the 15% that was paid late (but before October 15th)? Also, does this 90% rule appear in a specific IRS publication? I'd like to read up on it.
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Dylan Evans
•Yes, your client would be subject to the Failure to Pay Penalty on the 15% that was paid after the original due date, even though it was paid before the extension deadline. The penalty would be calculated from the original due date until the date of payment. The 90% threshold guidance appears in the Internal Revenue Manual (IRM) section 20.1.2, which covers penalty relief guidelines. It's not as prominently featured in public-facing publications, which is why it can be difficult to find. This is one of those technical details where tax software is actually implementing the correct rule that many preparers aren't aware of.
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StormChaser
Since you're dealing with tax software calculations, I was in the exact same position last month trying to figure out why my penalties weren't calculating correctly. I tried everything until I found taxr.ai (https://taxr.ai) which literally saved my sanity. I uploaded the client's tax documents and it flagged that I was confusing the estimated tax penalty rules with the failure to pay penalty provisions. The analysis confirmed what you're seeing in Ultratax is actually correct. The tool explained the different thresholds and how they apply, and even cited the relevant IRM sections that aren't easy to find on the IRS website. The explanation was crystal clear and I was able to confidently explain to my client why they weren't facing extra penalties.
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Dmitry Petrov
•Did you have to manually enter all the payment dates and amounts into taxr.ai? I'm wondering if it automatically identifies the payment timeline or if I need to input everything precisely. My client has made numerous partial payments and I'm trying to avoid manually calculating everything.
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Ava Williams
•I'm skeptical about these online tools. How does taxr.ai handle complex situations like amended returns or cases where payments were incorrectly applied by the IRS to different tax years? My experience is that software often misses nuances in penalty calculations.
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StormChaser
•You don't need to manually enter everything. The tool recognized all the payment dates from the transcript I uploaded and automatically mapped them to the correct tax periods. It's pretty smart about identifying payment patterns and allocations. For complex situations, I've found it handles amendments quite well. It analyzes the payment timeline against filing dates and can identify when payments were misapplied. I had a case where the IRS applied a payment to 2021 instead of 2022, and the analysis flagged this discrepancy immediately. The tool isn't just reading forms - it's interpreting the overall tax situation.
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Dmitry Petrov
Just wanted to follow up - I tried taxr.ai after seeing it mentioned here and it completely cleared up my confusion about the Failure to Pay Penalty vs. the Estimated Tax Penalty. The analysis confirmed that my client's situation (similar to the original poster's) was being calculated correctly by my software. What really helped was how it broke down the payment timeline and showed exactly why the 90% threshold was being applied. The tool even generated a clear explanation I could share with my client who was convinced they'd be hit with massive penalties. Definitely saved me hours of research and a potentially uncomfortable client conversation!
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Miguel Castro
Having dealt with penalty calculation issues for years, I've found that calling the IRS directly is sometimes the only way to get clarity. Of course, that's nearly impossible these days... until I found Claimyr (https://claimyr.com). Their service got me connected to an actual IRS agent in about 25 minutes when I had been trying for days on my own. I had them confirm this exact 90% rule for Failure to Pay Penalties on extended returns and got definitive confirmation from the agent. The video demo at https://youtu.be/_kiP6q8DX5c shows exactly how it works. Instead of sitting on hold for hours, their system calls you back when an agent is about to be connected. The IRS agent I spoke with was able to look at my specific case and confirm that the software calculation was correct.
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Zainab Ibrahim
•How does this actually work? I'm confused - does Claimyr have special access to the IRS phone lines? That seems impossible since the IRS phone system is notoriously difficult for everyone.
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Ava Williams
•Yeah right. There's no way some service can magically get through to the IRS when millions of people can't. I've tried calling dozens of times this filing season and it's been impossible. This sounds like a scam to collect your phone number or payment info.
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Miguel Castro
•It doesn't have special access - it uses an automated system that persistently redials and navigates the IRS phone tree until it gets through. Then when it reaches the hold queue, it waits in line for you and calls you when an agent is about to pick up. It's basically doing the tedious part for you. I was skeptical too. I've spent countless hours on hold with the IRS this season. The difference is their system can keep dialing and waiting when you can't. I'm not technically savvy enough to understand exactly how it works, but I can tell you that after trying unsuccessfully for three days to reach someone, I got a call back in under 30 minutes after using the service.
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Ava Williams
I need to eat crow here. After my skeptical comment, I was desperate enough to try Claimyr since I had a client with a penalty issue similar to this thread. I figured I had nothing to lose after spending 4 hours on hold with the IRS yesterday only to have the call dropped. Surprisingly, it actually worked. I got a call back in 45 minutes with an IRS representative on the line. The agent confirmed that the 90% rule does apply to the Failure to Pay Penalty for extended returns - it's in the Internal Revenue Manual but not clearly stated in most publications. This saved my client about $1,200 in penalties that another tax preparer had incorrectly calculated. I'm rarely impressed by services claiming to solve IRS issues, but this one delivered.
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Connor O'Neill
I work with multiple tax software platforms and this actually varies between programs. Ultratax handles it correctly, but I've seen ProSeries miscalculate this penalty in some cases. Always worth double-checking if you're using different software. Make sure your tax software settings have the correct payment dates entered, and verify that the extension was properly recorded in the system. Some programs require you to manually indicate that an extension was filed, or they'll calculate penalties as if the return was simply filed late.
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LunarEclipse
•Does this apply to corporate returns too? We have an S-Corp that paid 88% by the original due date and the rest by the extended date, but we're seeing penalty calculations that seem off.
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Connor O'Neill
•The rules are different for corporate returns. For S-Corporations, the 90% threshold doesn't apply in the same way. They generally need to pay 100% of the liability by the original due date to avoid the Failure to Pay Penalty, even with an extension. Extensions for businesses only extend the filing deadline, not the payment deadline. That's a common misconception. The 90% rule we're discussing in this thread is specific to individual returns (Form 1040) with certain conditions. Your software is likely calculating correctly if it's showing penalties for the S-Corp.
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Yara Khalil
Quick tip that helped me: if you go to the IRS Penalty Handbook in the Internal Revenue Manual (IRM 20.1.2), it specifically addresses reasonable cause criteria for penalty abatement. The 90% threshold is mentioned there as one of the factors that can indicate reasonable cause for relief from the Failure to Pay Penalty. So even if technically the penalty should apply, there's administrative guidance that essentially creates this 90% safe harbor that tax software like Ultratax is correctly implementing.
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Keisha Brown
•Thanks for pointing to the exact section! This explains why different software handles it differently - some are programming the strict letter of the law while others (like Ultratax) are incorporating the administrative practices the IRS actually follows. Definitely keeping this in my notes for future reference.
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NebulaNinja
This is a great discussion that highlights how complex tax penalty calculations can be! I've been a tax preparer for about 3 years and I'm still learning these nuances. What I find frustrating is that the IRS doesn't make these administrative practices more visible in their standard publications. I've had clients question penalty calculations before, and it's hard to explain why software is "right" when you can't easily find the supporting documentation. Does anyone know if there's a comprehensive resource that covers these types of administrative penalty relief guidelines? It would be helpful to have something to reference when clients ask about penalty calculations that seem counterintuitive based on the basic IRS forms and instructions. Also, for those mentioning the Internal Revenue Manual - is this something that's regularly updated, or are these guidelines pretty stable year to year?
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