SALT LAKE CITY — The American Civil Liberties Union has sued the state of Utah over the issue of gay marriage, saying the official decision to stop granting benefits for newly married same-sex couples has created wrenching uncertainty.

The lawsuit filed Tuesday says the state has put hundreds of gay and lesbian couples in legal limbo and prevented them from getting key protections for themselves and their children.

“They’ve put a giant question mark over the lives of all these people that have married,” said John Mejia, legal director for the ACLU in Utah.

Utah Gov. Gary Herbert “has said throughout this process that his responsibility is to follow the law,” spokesman Marty Carpenter said. “That is exactly what the administration is doing, and we respect the rights of those who disagree to take their grievances before a judge.”

More than 1,000 gay and lesbian couples rushed to marry after a federal judge in Utah overturned the state’s same-sex marriage ban on Dec. 20. U.S. District Judge Robert Shelby ruled that the same-sex marriage ban violates gay and lesbian couples’ constitutional rights. Those weddings came to a halt on Jan. 6 when the U.S. Supreme Court granted Utah an emergency stay – something two lower courts denied them.

After the Supreme Court issued the stay, Herbert told state agencies to hold off on moving forward with any new benefits for the couples until the courts resolve the issue. Agencies were told not to revoke anything already issued, such as a driver’s license with a new name, but they are prohibited from approving any new marriages or benefits. More recently, the state tax commission announced that newly married gay and lesbian couples can jointly file their taxes for 2013.

The state made clear it was not ordering agencies to void the marriages, saying instead that validity of the marriages will ultimately be decided by the Denver-based 10th U.S. Circuit Court of Appeals.

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