Small waves generated by the undersea quake were detected in several parts of the sprawling archipelago, local authorities said, although there were no reports of casualties or major damage and the tsunami warning was lifted after a short while.
Nevertheless, the prospect of a major tsunami set nerves on edge in one of the most seismically active countries in the world, almost a decade after quake-triggered destructive waves devastated western Aceh province.
The tsunami of December 26, 2004, left more than 170,000 people dead in Aceh, on Sumatra island, and tens of thousands more in countries with coasts on the Indian Ocean.
Saturday's tremor struck northwest of the town of Kota Ternate, at 0231 GMT, the US Geological Survey said.
"Tsunami waves are possible for coasts located within 300 kilometres," said the Pacific Tsunami Warning Center.
The centre also warned of small tsunami waves in the Philippines, Japan, Taiwan and islands in the South Pacific.