The quake had a preliminary magnitude of 7.0, but at a depth of 86 miles was too far below the earth's surface to cause a tsunami, the Pacific Tsunami Warning Center said.
Saturday's quake came as Indonesia is still recovering from a devastating earthquake last month that killed more than 1,000 people on western Sumatra.
The U.S. Geological Survey says Saturday's quake - the second strong temblor in two days - was located 225 miles southeast of Ambon in the Maluku islands in the Banda Sea.
The shaking was strong and people ran to higher ground fearing a tsunami, said Ian Kotualubun, an official with Indonesia's Meteorology and Geophysics Agency in Saumlaki, the area closest to the epicenter, about 1,700 miles east of the capital, Jakarta.
Indonesia sits above a series of fault lines that make the vast island nation one of the most earthquake-prone places in the world.
A massive quake off the coast of Indonesia's Aceh province caused the 2004 Indian Ocean tsunami that killed 230,000 people, half of the victims on Sumatra island.