The U.S. Department of Justice filed the lawsuit on April 22 after Google had refused legal but controversial demands from the FBI for confidential user data, CNET reported Friday.
The FBI demands were based on so-called National Security Letters, a secret electronic data-gathering process that can be carried out without a judge's approval.
The NSL technique -- which is intended to be limited to national security investigations, not routine criminal probes -- has already been declared unconstitutional in an unrelated court case, CNET reported.
Because Google was already challenging NSLs in a lawsuit filed weeks earlier in California, it asked U.S. District Judge Susan Illston in San Francisco to throw out the New York NSL.
Illston declined, ruling the issue "is more squarely raised" in the New York litigation.
Cindy Cohn, legal director of the Electronic Frontier Foundation, which has filed its own lawsuit challenging NSLs on behalf of an unnamed telecommunications company, said it was unclear why Google has decided to take on the Justice Department at this point.
"My instinct tells me that Google doesn't pick a fight with the government easily," she said. "There's probably something going on here that's different from a run-of-the-mill NSL."