WASHINGTON — The government on Thursday said that all legally married gay couples will be able to file joint federal tax returns even if they reside in states that do not recognize same-sex marriages.

The decision came in rules issued by the Treasury Department and the Internal Revenue Service designed to implement the tax aspects of the Supreme Court’s decision in June that invalidated a section of the 1996 Defense of Marriage Act.

“Today’s ruling provides certainty and clear, coherent tax filing guidance for all legally married same-sex couples nationwide,” Treasury Secretary Jacob Lew said in a statement.

“This ruling assures legally married same-sex couples that they can move freely throughout the country knowing that their federal filing status will not change,” Lew said.

Chad Griffin, president of the Human Rights Campaign, the nation’s largest gay rights group, praised the government’s action.

“With today’s ruling, committed and loving gay and lesbian married couples will now be treated equally under our nation’s federal tax laws, regardless of what state they call home,” Griffin said in a statement.

The Treasury said that with the new rules, same-sex couples will be treated as married for all federal tax purposes including income and gift and estate taxes.

The rules will cover all federal tax provisions where marriage is a factor including the taxpayer’s filing status, personal and dependent exemptions and standard deductions.

The new rules will cover any same-sex marriage legally entered into in any state where such a marriage is recognized. It will also cover such marriages recognized by U.S. territories, foreign nations and the District of Columbia.

The government said that the statute of limitations for filing a refund claim was generally three years from the date the return was filed or two years from the date the tax was paid, whichever was later. As a result, the government said that refund claims can still be filed for tax years 2010, 2011 and 2012.

The new IRS and Treasury regulations follow rules changes and guidance that have already been issued by other federal agencies including the office of Personnel Management and the departments of Defense and Health and Human Services.

The Supreme Court ruling came in a case filed by Edie Windsor, a resident of New York, who was forced to pay federal estate taxes after the death of Thea Spyer, her lesbian spouse.