In a filing with the court, the administration says Section 3 of the Defense of Marriage Act denies legally married same-sex couples many federal benefits that are available only to legally married heterosexual couples. Federal tax and Social Security survivor's benefits are among them.
In its brief, the administration said the provision "violates the fundamental constitutional guarantee of equal protection."
The brief was filed as the justices prepare to hear arguments next month in a challenge to the 1996 law.
President Barack Obama last year said he personally supports gay marriage. He said in last month's inaugural address that the law should treat gay people like anyone else.