Scores of migrants are now being removed from a Brooklyn elementary school gym — just days after the site was controversially set up as a temporary asylum seeker shelter, The Post has learned.

The asylum seekers were set to be removed from PS 188 in Coney Island and moved to an undisclosed location in Manhattan by the end of Wednesday, sources said.

Other school gym shelters that haven’t yet been widely utilized — including Williamsburg’s PS 17/MS 577 and PS 18 — are also expected to be shut down soon, according to those familiar with the situation.

“The plan is to make sure school gyms are not used as shelters,” City Councilman Ari Kagan told The Post soon after being alerted to the change in plans by NYC Emergency Management.

Fellow Councilman Justin Brannan also chimed in on Twitter, confirmed the closure of the PS 188 temporary shelter.

“Plan is to no longer use this site for temporary shelter,” he tweeted. “Our schools should not be used for this purpose.”

A school safety officer at PS 17/MS 577 told The Post that dozens of green cots that had been erected inside the gym at the beginning of the week had already been taken down by Wednesday afternoon.

“All the cots are packed up and bagged up,” the officer said, adding they’ll be picked up by officials after the school day ends.

“The order is ‘dismantle and sanitize’ so the kids can go back in the gym,” the officer added. “It’s done. Finito.”

The decision comes just days after it emerged 20 school gyms were being eyed to hold migrants — a move that sparked fury among parents.

Outraged parents spent Monday to Wednesday protesting outside the Williamsburg schools, as well as PS 172 in Sunset Park, which was also set up with cots earlier this week.

It wasn’t immediately clear if the PS 172 gym was also being cleared out Wednesday.

It also isn’t yet clear if the Adams administration’s abrupt reversal was due to the intense backlash from parents.

City Hall didn’t immediately respond to The Post’s request for comment.