The petition filed by the Health Department in Commonwealth Court alleges that D. Bruce Hanes, the register of wills in Montgomery County, "repeatedly and continuously" flouted the law. As of Tuesday afternoon, the county had granted 34 licenses and registered six same-sex marriages.
"There is no limit to the administrative and legal chaos that is likely to flow from the clerk's unlawful practice of issuing marriage licenses to those who are not permitted under Pennsylvania law to marry," the lawsuit said.
Pennsylvania is the only northeastern state without same-sex marriages or civil unions. Hanes began issuing licenses to same-sex couples shortly after the U.S. Supreme Court struck down part of the federal Defense of Marriage of Act.
At the time, Hanes said he wanted to "come down on the right side of history and the law." He declined to comment Tuesday on the pending litigation.
The Health Department, which oversees marriage licenses for the state, said in the lawsuit that Hanes' actions are interfering with the agency's administrative responsibilities and would likely lead to illegal claims for benefits. A department spokeswoman also declined to comment.
The developments come the same day that Republican Gov. Tom Corbett's office indicated that it would defend the state's marriage law in a separate legal challenge filed by the American Civil Liberties Union.
Attorney General Kathleen Kane, a Democrat who supports same-sex marriage, had said earlier this month that she wouldn't defend the state in that suit because she believes the law to be unconstitutional.
On Tuesday, Corbett's general counsel wrote in a letter to Kane's first deputy that the governor's office would defend the law. But General Counsel James Schultz said that Kane's refusal "establishes a very troubling precedent."
"This will create chaos and uncertainty - not unlike what we are seeing in the unlawful actions" of Hanes in Montgomery County, Schultz wrote.
A 1996 state law defines marriage as a civil contract in which a man and a woman take each other as husband and wife. It says same-sex marriages - even if entered legally elsewhere - are void in Pennsylvania.
The ACLU has sued to have the law overturned. The state was granted an extension to respond to that lawsuit on Monday. Officials must now respond by Sept. 16.
Recent polls show a majority of state residents favor gay marriage in Pennsylvania, even though bills to legalize it have gone nowhere in recent years in the Legislature.