The bodies of Frans Koagow, 64, and his wife, Femy Kumendong, 73, were discovered by their grandson in the priest's home on Sulawesi island over the weekend with deep wounds to their heads and necks, said local police chief Aridan Roero.
Authorities have yet to determine a motive, he said, and no suspects have been named.
"We're still investigating," Roero said. "It's too early to say anything."
More than 90 percent of Indonesia's 235 million people are Muslims, but Sulawesi - the scene of religious clashes that left up to 2,000 people dead from 1998 to 2002 - has a large Christian population.