WASHINGTON — While the tax package that Congress passed New Year’s Day will protect 99 percent of Americans from an income tax increase, most of them will still end up paying more federal taxes in 2013.

That’s because the legislation did nothing to prevent a temporary reduction in the Social Security payroll tax from expiring. In 2012, that 2-percentage-point cut in the payroll tax was worth about $1,000 to a worker making $50,000 a year.

The Tax Policy Center,a nonpartisan Washington research group, estimates that 77 percent of American households will face higher federal taxes in 2013 under the agreement negotiated between President Barack Obama and Senate Republicans. High-income families will feel the biggest tax increases, but many middleand low-income families will pay higher taxes, too.

Households making between $40,000 and $50,000 will face an average tax increase of $579 in 2013, according to the Tax Policy Center’s analysis. Households making between $50,000 and $75,000 will face an average tax increase of $822.

“For most people, it’s just the payroll tax,” said Roberton Williams, a senior fellow at the Tax Policy Center.

A package of tax cuts first enacted under President George W. Bush was scheduled to expire Tuesday as part of the “fiscal cliff.” The Bushera tax cuts lowered taxes for families at every income level, reduced investment taxes and the estate tax, and enhanced a number of tax credits, including a $1,000-per-child credit.

The package that passed Tuesday by the Senate and House extends most of the Bush-era tax cuts for individuals making less than $400,000 and married couples making less than $450,000.

Obama said the deal “protects 98 percent of Americans and 97 percent of small-business owners from a middle class tax increase. While neither Democrats nor Republicans got everything they wanted, this agreement is the right thing to do for our country.”

The income threshold covers more than 99 percent of all households, exceeding Obama’s claim, according to the Tax Policy Center. However, the increase in payroll taxes will hit nearly every wage earner.

Social Security is financed by a 12.4 percent tax on wages up to $113,700, with employers paying half and workers paying the other half. Obama and Congress reduced the share paid by workers from 6.2 percent to 4.2 percent for 2011 and 2012, saving a typical family about $1,000 a year.

Obama pushed hard to enact the payroll tax cut for 2011 and to extend it through 2012. But it was never fully embraced by either party, and this time around, there was general agreement to let it expire.

Sabrina Garcia, a 35-yearold accounting assistant from Quincy, Mass., who together with her husband made about $102,000 last year, said the payroll tax increase equated to “about $200 a month for my family.”

“That’s a lot of money for us. It means we will have to cut back.” She said in an email exchange that she most likely would postpone buying a new computer. “And forget about being able to save money,” she added.

The new tax package increases the income tax rate from 35 percent to 39.6 percent on incomes above $400,000 for individuals and $450,000 for married couples. Investment taxes increase forpeople who fall in the new top tax bracket.

High-income families will also pay higher taxes this year as part of Obama’s 2010 health-care law. As part of that law, a new 3.8 percent tax is being imposed on investment income for individuals making more than $200,000 a year and couples making more than $250,000.

Together, the new tax package and Obama’s health-care law will produce significant tax increases for many highincome families.

For 2013, households making between $500,000 and $1 million will get an average tax increase of $14,812, according to the Tax Policy Center analysis. Households makingmore than $1 million will get an average tax increase of $170,341.

“If you’re rich, you’re almost certain to get a big tax increase,” Williams said.

For married couples filing jointly, the deduction limits apply to incomes above $300,000, while the top tax rate kicks in above $450,000. “Income” in this context is a technical term, referring only to the portion of income subject to taxation after exemptions and deductions.

Few households with actual incomes of less than half a million dollars will face a tax increase. The Tax Policy Center calculated that less than 5 percent of families earning $200,000 to $500,000 will actually pay more.

The deal passed by the Senate and House will impose fewer limits on deductions than the White House plan. It will tax income from dividends at a flat rate of 20 percent, rather than the same marginal rate as earned income. Affluent households will pay the new 39.6 percent rate only on income above $450,000. They and everyone else still will pay lower rates on income below that threshold.

The estate tax will not apply to the first $5 million of an inheritance, extending the current exclusion rather than reverting to the $3.5 million threshold that Obama initially favored. However, wealth above that amount will be taxed at a rate of 40 percent rather than the previous rate of 35 percent.

The Obama administration did win a five-year extension on tax breaks for lower-income families, including the child tax credit and earned-income tax credit. Those credits eliminate income tax liability for many lower-income families. In many cases, the government actually makes a direct payment to the family to help offset the burden of payroll taxation - up to $1,000 a child under the child credit and up to $5,900 total under the earned income credit.

The deal also will restore unemployment benefits for about 2 million Americans.

People who can’t find work and have already received government checks for thestandard period of 26 weeks have been able to stay on the rolls for up to an additional 47 weeks. But financing for that program, which is aimed at the states with the highest unemployment rates, expired Saturday.

Under the terms of the deal, people who are eligible would receive any missed benefits retroactively.

The deal also includes new rules for the alternative minimum tax, which threatened this year to impose higher taxes on roughly 30 million households.

The tax was created in the 1960s to set a lower limit on the taxes paid by the most affluent households, but the eligibility threshold was not indexed to inflation, so it theoretically encompasses a larger share of households with each passing year. Congress has repeatedly passed short-term increases in the threshold; the deal will make those increasesautomatic, obviating the annual ritual.

That is small consolation for middle-income Americans such as Joe Interlandi, 61, a long-haul trucker who on Tuesday was driving a load of tomatoes from Florida to Los Angeles.

Interlandi, writing from a rest stop, said he understood the need for higher taxes. He would rather pay more now than impose higher taxes on his children and grandchildren, he said.

But Interlandi, who estimated that he worked 100 hours many weeks, added that the payroll tax increase still meant that he will need to spend even more time on the road.

Describing things he will have to cut back, he wrote, “Family outings like vacations, and time together.” Information for this article was contributed by Stephen Ohlemacher of The Associated Press and by Binyamin Appelbaum and Catherine Rampell of The New York Times.

Front Section, Pages 1 on 01/03/2013