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You may need to contact the IRS to have the payments made through EFTPS applied to the correct year in their system.
If you have filed your 2016 tax return reporting the estimated payments made, you do not need to file an amendment. Additionally, if you paid all of your estimates in one lump sum at the beginning of the year (on or before the April 15 deadline for the first payment), there will be no penalties assessed.
The best way to contact the IRS (if you are able to do so) is to use your local IRS branch. Please see this website (https://www.irs.gov/help-resources/contact-your-local-irs-office) for more informaiton about online services or to locate your local IRS office.
If you are unable to get to your local IRS office, you can contact EFTPS customer service at 800-555-4477.
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