Frans Koagow, 64, and his wife, Femy Kumendong, 73, were found in the priest's home in Manado city, North Sulawesi province, on Saturday with deep slash wounds to their heads and necks, provincial police spokesman Benny Bella said.
'The priest was cut from behind in the neck while his wife was cut in the head while she lay down sick with a stroke,' Mr Bella said.
'The priest had been squatting down to tie his shoes when he was attacked... there was no time for him to fight back.'
Mr Bella said police were looking for suspects but were unsure how many people were involved in the attack.
'We found a machete but we don't know if it was one that was used in the murder,' he said.
North Sulawesi province is a stronghold of mostly Protestant Christianity in Indonesia, where Muslims make up roughly 90 per cent of the national population.