The scheme aimed to help 2,570 workers evade a total of $2.1 billion won ($2.28 million) in tax in 2005-2006, the paper said.
Donations to charities, schools and religious organisations are tax-deductible up to a certain amount.
Some monks even distributed pamphlets advertising the fake donation service, prosecutors were quoted as saying.
"These temples were businesses selling fake receipts rather than religious organisations,'' said prosecutor Jo Myeong-Sun.
The finance ministry said it plans to crack down on the racket, including tougher punishment for offenders.