Police said Monday the church's former organist confessed he removed it last week for safekeeping.
Worshippers had struggled to understand how and why anyone would take the massive 200-pipe instrument from St. Justin's, which closed last month after merging with another church.
Authorities say the organist had a key to the building in the city's Mount Washington neighborhood and was worried the organ would be damaged by the cold of winter.
The church's pastor, Father Michael Stumpf, says taking the organ was an imprudent and terrible mistake but not a criminal one so the church is choosing to forgive and not press charges.
