A Brooklyn church is ­suing its former rector to recover tens of thousands of dollars that vanished from an escrow account to which he had access, according to a lawsuit.

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Arefiev, 47, was removed from the church last year. He is now a rector’s assistant at the Unexpected Joy Church on Staten Island.

He told The Post he never stole a dime, and that the cash was used to pay a real- estate consultant.

“My dream is to build a new church,” he said.

A lawyer for the church had no comment.