NOTICE OF DEFICIENCY IRS: How to Pay Notice of Deficiency IRS

NOTICE OF DEFICIENCY IRS: How to Pay Notice of Deficiency IRS
NOTICE OF DEFICIENCY IRS: How to Pay Notice of Deficiency IRS

A notice of deficiency is usually triggered by tax information received from a third-party filer, such as an employer or financial institution that does not match the information provided by the taxpayer. 

A notice of deficiency is triggered by a taxpayer’s failure to timely respond to or successfully appeal a preliminary assessment letter, known as a 30-day letter.

What Is Notice Of Deficiency IRS?

An IRS Notice of Deficiency is a legal notice from the IRS that informs a taxpayer that their previous tax payment was insufficient or insufficient.  This is sent when the IRS determines that a taxpayer’s income information was omitted from their tax return and therefore their tax payment was less than it should have been.

For example, if a taxpayer doesn’t file a tax return for a particular year, but the IRS believes they owe tax for that year, the IRS will send a warning notice to the taxpayer asking them to file a tax return.

If a taxpayer fails to file a tax return or otherwise fails to satisfy IRS requests, the IRS will ultimately determine the taxpayer’s own liability for the year and send the taxpayer a notice of deficiency.

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How Does Notice Of Deficiency IRS Work?

A notice of deficiency is sometimes called a 90-day letter because it gives the taxpayer 90 days to appeal the tax assessment in tax court.  The 90-day period within which a petition can be filed is set by law and cannot be extended. 

The 90-day period is counted from the date the deficiency notice is sent to the taxpayer’s last known address.  The law requires the IRS to include the last day the petition can be filed directly in the notice of deficiency. 

Until the later of 90 days or the decision of the Tax Court is final, whichever is later, the IRS is prohibited from conducting any assessment or collection activity. It is important to note that a deficiency notice is not a tax invoice. 

However, if the taxpayer does not sign a Waiver Form 4089 agreeing to the changes or file a petition with the Tax Court within the 90-day period, the IRS will assess the tax, penalties, and interest on the notice of deficiency and send the notice to the account.  This is one of the events that precedes and initiates the IRS’s collection efforts.

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How To Disagree With the Notice of Deficiency

File a petition with the US Tax Court

The first option is to challenge the claim by filing a lawsuit in tax court within 90 days of the date the deficiency notice was sent. 

The Tax Court must reassess the tax liability proposed by the IRS.  During the inspection period, the tax office is prohibited from assessing the taxpayer or enforcing tax debts.

File an appeal

A taxpayer may also appeal a tax proposal by providing the IRS with a written statement at the time of filing the appeal.  The written statement must include additional information to support their case, including records of income and expenses for the tax year.

The taxpayer can also ask the third party that provided the information – such as an employer or financial institution – to submit corrected records that show the correct information about the taxpayer’s income for the year.

Call the IRS

The taxpayer can also call the IRS at the number listed in the notice to speak directly with an IRS representative.  They can ask questions about why they received the notice and provide information about incorrect reporting on the tax return.

However, providing information over the phone is not sufficient, and the taxpayer will still need to provide information by sending a signed written statement explaining their disagreement with the proposal.

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What to Do if You Agree With The Notice of Deficiency

If you receive a CP2000 or CP3219A and realize that yes, you made a mistake and you agree with the IRS that you owe more tax and you no longer need to amend your return, simply sign Form 5564, Notice of Deficiency – Waiver and send it back to the agency. 

There is no need to amend your tax return unless you discover additional income, credits or expenses.  In that case, file Form 1040-X to include the new information on your original return.

Remember to pay the additional taxes as specified in the Notice of Deficiency.  By the way, because you are late with your payment, you will also have to accrue penalties and interest on the unpaid tax debt.

If you are notified of a tax reduction, you can consider yourself lucky.  Just remember to submit Form 5564 by the deadline.

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Notice of Deficiency IRS Appeal

Conversely, taxpayers who have timely appealed to the Tax Court can make arguments as to why the proposed adjustments are erroneous.  Without a doubt, the substance of the petition is extremely important.  And failure to properly appeal an IRS decision can be costly.

After you respond to the IRS’s response to your petition, you will be given an opportunity to settle the matter with the IRS.  The IRS Appeals Office will contact you to schedule a hearing.  Sometimes, the IRS agrees with its position when the case goes to the appeals office. 

In other cases, the IRS will not budge when meeting with the taxpayer about the new amount owed to the agency.  Most of the times, the IRS will settle with a taxpayer only if the following problems exist:

  • The IRS is concerned about evidence admissible in court
  • They are concerned about the Tax Court’s factual findings
  • The IRS is concerned about the Tax Court’s interpretation of the law

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How to Pay Notice of Deficiency IRS

If you are required to pay a new amount determined by the IRS, you can create a plan to notify the IRS of the deficiency payment. 

The IRS offers payment plan options for taxpayers who cannot afford to pay the full amount of taxes when they file their tax return. 

It is important to note that interest will accrue on the new amount until it is fully paid by the agency.  This means that even if you set up a payment plan, interest will accrue on the full amount owed until the payment plan is completed.  The IRS accepts payments by the following methods:

  • Credit cards
  • Debit cards
  • Check
  • Payroll deductions

If you agree with the changes published by the IRS on Form 5564 Notice of Deficiency Waiver, you must sign the IRS Notice of Deficiency Response Form and complete and submit Form 9465 (Request for Installment Agreement) to adjust your payment plan  at the IRS.

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Notice of Deficiency IRS Amended Return

When you are issued a tax court notice of deficiency, you do not need to make changes to your tax return with the IRS as long as the information in the “changes to your tax return” section of the notice is correct. 

You only need to amend your tax return if you have additional income to report, additional expenses to report, or credits to report to the IRS.

If you have additional expenses, income, or credits to report to the IRS, be sure to fill out Form 1040-X (Amended U.S. Individual Income Tax Return) and write CP3219 at the top of the return so the agency knows you’re making a change. 

The amended return should be attached to Form 5564. The amended return should be mailed or faxed to the address or number listed on the deficiency waiver notice and should not be sent to any other IRS office.


Many taxpayers panic after receiving a notice or letter from the Internal Revenue Service, especially when it comes to conflicting tax returns.  While an IRS notice of deficiency can be alarming to a taxpayer, it also requires a response within 90 days.  But taxpayers can appeal to the Internal Revenue Service and challenge it in court if they disagree with the amendments.

The IRS can cross-reference your tax return and financial institution and employer reports.  This committee scrutinizes both records before suggesting an adjustment.  But what is a shortage notice?  The commission informs taxpayers in case of inconsistency of information or lack of necessary funds with an official notice of shortage.

Notice of Deficiency IRS FAQs

What Is A Waiver Of Deficiency?

A formal Notice of Deficiency Waiver is the form you will use to tell the IRS that you agree with the proposed amount of additional tax.  You can indicate your agreement by signing and returning Form 5564. You will receive a bill for your IRS underpayment notice shortly.  Just remember that you never sign Form 5564 if you only partially agree with the IRS’s opinion.

What Is IRS Form 5564?

IRS Form 5564 is attached when the federal tax authority sends IRS Notice CP3219A.  The form is known as a Notice of Waiver of Deficiency and is used when the taxpayer does not object to an IRS proposal.  If the taxpayer accepts the IRS offer, the taxpayer must sign the waiver and send it to the IRS.

What To Do If You Cannot Pay Notice of Deficiency IRS In Full?

If your tax bill is more than you can afford to pay in one go, contact the IRS to work out a plan to pay off your tax debt.  You have several plans at your disposal, depending on what you can afford to pay and how long you need to pay off the entire amount.

  Remember that you will accrue interest on any outstanding balance until you pay it in full.  Still, it’s better than having your property seized and other penalties the IRS can impose.  Payment plans are available for different time periods.

  Remember that you will accrue interest on any outstanding balance until you pay it in full.  Still, it's better than having your property seized and other penalties the IRS can impose.  Payment plans are available for different time periods.

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