Gov. Mike Pence's decision, first announced in a memo from chief counsel Mark Ahearn, applies only to state agencies that report to his governor's office and would affect state services controlled by those agencies, such as food stamps or the ability to file jointly for state taxes.
Hundreds of couples were married from June 25, when a U.S. district court judge struck down the state's gay marriage ban, to June 27, when a federal appeals court stayed the decision.
Pence, a Republican, told reporters at a Statehouse event Wednesday that the state was only abiding by the decision of the federal appeals court that stayed the earlier ruling that struck down Indiana's gay marriage ban.
The Indiana attorney general's office, which is handling the court challenges, had no immediate comment.
Also Wednesday, Utah opted to challenge a different federal appeals court ruling on its gay marriage ban, taking it to the U.S. Supreme Court. Utah Attorney General Sean Reyes' office said in a statement the appeal will be filed in the coming weeks to get "clarity and resolution" from the highest court.
American Civil Liberties Union of Indiana Legal Director Ken Falk said Wednesday he believes Indiana is wrong and the marriages are legal.
"During the time they were married they were lawfully married and the fact that the law, in effect, changed subsequent to their marriage does not void their marriages," Falk said in an email to The Associated Press.
The sole exception to the appeals court stay in Indiana was an order for the state to recognize the out-of-state marriage of Amy Sandler and Nikole Quasney of Munster; Quasney is dying of ovarian cancer. The memo said the state would follow that order.
Senate Democratic Leader Tim Lanane, D-Anderson, called the governor's directive "excessive" and that it only confused the issue.
"I believe the governor has jumped to conclusions that don't clearly come from the order of the 7th Circuit Court of Appeals," he said in a statement.
Democratic Marion County Clerk Beth White, whose office performed more than 450 same-sex weddings, called the governor's decision disheartening and disappointing."
"Gov. Pence owes these couples an explanation on why he continues to deem them as second class citizens," she said in a statement.