Police said the 34-year-old had confessed to removing marble slabs covering the graves of three leaders of the Cypriot Orthodox church from the late 19th and early 20th century.
They also said skeletal remains had disappeared from one of the tombs, but that the remains from another, briefly thought to have been taken, had in fact been re-buried elsewhere years ago.
The suspect, who had not been charged, was arrested after turning up at a police station with a bag of human excrement, which he threw at police officers. He denied removing any human remains from the tombs.
"From what he says, it appears he has issues with the Church and holy grounds," said Kypros Michaelides, divisional police commander in Nicosia.
Most Greek Cypriots belong to the Church of Cyprus, which is an independent branch of the Eastern Orthodox Communion. Last December thieves snatched the remains of late president Tassos Papadopoulos and hid them in another cemetery. The body was found this month and police say two people suspected of stealing the corpse for ransom are in custody.
