The withholding tables, however do not take into account taxpayers with multiple jobs or married couples in which both people work. They also don't take into account Social Security recipients with jobs that provided taxable income.
The Social Security Administration sent out $250 payments to more than 50 million retirees in the spring as part of the economic stimulus package. The payments were meant to provide a boost for people who didn't' qualify for the tax credit.
However, they went to many retirees who also received the credit. Those retirees will have the $250 payment deducted from their tax credit -- but not until they file their tax returns next year, long after the money may have been spent.
"While implementing a credit through reduced withholding is an effective way to provide economic stimulus evenly throughout the year, it is difficult to account for everyone's circumstances," said J. Russell George, the Treasury inspector general for tax administration. "More than 10 percent of all taxpayers who file individual tax returns for 2009 could owe additional taxes."
Separately, the IRS estimated that about 65,000 taxpayers could face penalties for not withholding enough taxes in 2009 because of the overly generous tax credits. However, those taxpayers will be eligible to have the penalty waived, IRS spokeswoman Michelle Eldridge said.
The tax credit is also available for 2010. Russell said the problems will continue in 2010 if they are not resolved.
The credit pays workers 6.2 percent of their earned income, up to a maximum of $400 for individuals and $800 for married couples who file jointly. Individuals making more than $95,000 and couples making more than $190,000 are ineligible.
"Making Work Pay was designed to deliver much needed boosts to the paychecks of 95 percent of all working Americans," said Nayyera Haq, a Treasury Department spokeswoman. "Since enactment, more than 110 million families have benefited from as much as $60 in additional take home pay each month to put toward their family budgets, serving as a steady boost to spending and consumption."
For many, the new tax tables will simply mean smaller-than-expected tax refunds next year. The average tax refund this year was about $2,800. A little more than three-quarters of the 143 million taxpayers filing a return last spring received refunds, according to the IRS.
The IRS, in a response to the audit, advised taxpayers to check their withholding throughout the year to make sure they don't get hit with an unexpected tax bill.
"The withholding system must approximate the tax liability of tens of millions of Americans, and therefore, cannot be tailored precisely to fit every individual situation," Richard Byrd Jr., commissioner of the IRS' wage and investments division, wrote in the agency's response to the report.
The IRS has a calculator on its Web site so taxpayers can check whether they are withholding an appropriate amount of taxes from their pay. But with only a month and a half remaining in the year, it's getting late for taxpayers to make adjustments.
On the Web:
IRS withholding calculator: http://www.irs.gov/individuals/article/0,,id=96196,00.html