The 18-foot pipes were among about 50 stored in the basement at First Churches in Northampton during the sanctuary's renovation.
The Rev. Peter Ives estimates the damage at close to $15,000. But he says the organ can be played without the pipes. Ives says the church will not press charges.
The man apparently mistook the pipes for rolled-up rugs and slept on them. He is a homeless man who was in the church for a job counseling meeting.
The congregation traces its history to the 17th century, and was home to 18th century preacher Jonathan Edwards.