A Florida judge ruled against Gov. Ron DeSantis on Wednesday and is allowing schools to issue mask mandates while the appeals court sorts out the legality of the governor’s ban.

Leon County Judge John Cooper ruled to vacate an automatic stay given to the state after it appealed his previous decision stating that DeSantis’s executive order banning school mandates is unconstitutional, according to Fox 13 Tampa Bay.

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Cooper said he believes this is the first time he has vacated a stay.

"We are not in normal times," he said. "We are in a pandemic. We have children who cannot be protected by a vaccination."

The governor’s order allowed parents to decide if they want their kids to wear masks to school rather than have local school districts make the decision, prompting a lawsuit brought by a group of parents in favor of school mask mandates.

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"No surprise here that Judge Cooper concluded that he is unlikely to be overruled on appeal," DeSantis Communications Director Taryn Fenske told Fox News. "We unsurprisingly disagree. Today we plan to file our emergency motion to reinstate the stay, and we anticipate the appellate court will rule quickly, much like during the school re-opening case last year."

DeSantis said last week he believes the state will win in the 1st District Court of Appeal in Tallahassee because of a new state law, the Parents Bill of Rights, which he said gives parents the final authority on their children’s health.

"We'll end up getting it back," the governor told reporters. "Obviously [Cooper's ruling], it’s problematic."

DeSantis said he wants to stand with parents regarding their ability to decide what’s best for their children.

"We think it’s important that they are given the ability to opt out" of wearing a mask, DeSantis said.

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School boards in 13 districts in the state have voted to defy the order, choosing to require masks because of the virus resurgence, and they faced possibly having their salaries withheld. The Biden administration had promised federal funds for any district that lost money for requiring masks.

DeSantis’ office did not immediately respond to a request for comment from Fox News.

Fox News’ Brie Stimson contributed to this report