Incorrect W-4, Underpaid taxes: What now?

I just found out today that my employer has not been withholding federal taxes on my paycheck since mid-February 2013.  I received a raise in that time frame, so the increase in the amount I was being paid did not make my radar, and I just found out today when I needed to get my annual salary for another position.

I don't have the money to pay everything that should have been withheld during the year, but I can pay the amount I owe by April 15 next year.  I am concerned, though, about having to pay penalties and/or fees since I have not had any federal taxes withheld during most of the year.

What should I do?  I tried calling the IRS today, but their phone lines are busy to the point where they're not even answering calls right now.  I want to make right by this; I've always paid all of my taxes owed and never been late.  I normally get a large refund, in fact, because I always file my W-4 as single with no exemptions.  My employer says they don't have any kind of auditing trail showing how it got changed, and it's done electronically.  I don't want to get into trouble, but at the same time, I don't want to get screwed over and tagged with a bunch of penalties and fees for something that was a mistake.
You may be able to get the IRS to waive any interest and penalties they might assess. But...I imagine you got some kind of "paycheck stub" each pay period that showed your gross income and the various withholdings. Be sure to also check your state tax, Social Security and Medicare withholdings.
  • They have been withholding Medicare and Social Security, as well as state taxes, thank goodness.  Just not federal taxes.  And they don't send me paycheck stubs, but it's available on their intranet site electronically.  Like I said, though, I got a raise in February, so when I started getting more money direct deposited, I didn't think much about it.  I didn't know that it wasn't supposed to be that much.
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