A federal judge on Sunday blocked the Obama administration’s directive that school children be allowed to use bathrooms and other facilities that align with their gender identity regardless of biological gender -- siding, for now, with 13 states and agencies challenging the controversial order.

U.S. District Judge Reed O’Connor did not rule on the underlying challenge itself. The order means that the administration's directive will be blocked while the case itself plays out. 

O'Connor, a Texas-based federal judge, determined the administration had "failed to comply" with federal rules for issuing such directives -- including "notice and comment requirements." 

The Department of Justice responded to the ruling in a statement, saying it was "disappointed in the court’s decision" and is reviewing its options. 

The challenge by the states and agencies, led by Texas, is the latest battle between the federal government and various states opposed to the policy changes.

The White House in May told the nation's public school districts they must allow transgender students to use bathrooms and other facilities like locker rooms matching their chosen gender identity or risk losing federal funding.

"We will not yield to blackmail from the president of the United States," Texas Lt. Gov. Dan Patrick said in response to the order. "This goes against the values of so many people."

The other states involved are Alabama, Arizona, Georgia, Kentucky, Louisiana, Maine, Mississippi, Oklahoma, Tennessee, Utah, West Virginia and Wisconsin.

Other states last month launched a similar suit to stop the new bathroom policy in public schools. They are: Arkansas, Kansas, Michigan, Montana, Nebraska, North Dakota, Ohio, South Carolina, South Dakota, and Wyoming.

In suburban Chicago, 51 families also have challenged a government directive on the issue, while earlier this month the Supreme Court granted a temporary injunction blocking an order that would have allowed a Virginia high school student who was born female but identifies as male to use the boys' restroom.

Fox News’ Shannon Bream and Matthew Dean contributed to this report.