The Reverend Rafal Jarosiewicz published his apology on Facebook.
He said the burning of books and other items linked to magic and the occult was "unfortunate".
Mr Jarosiewicz and other priests have drawn criticism after they burned books and items brought by parishioners on Sunday before a church in Gdansk, saying they were doing away with evil influences.
He was fined and an anti-smog group has contacted prosecutors about the open fire.
The book-burning comes as Poland's influential Catholic Church is grappling with revelations about the scale of paedophilia among its priests.
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