The quake struck at a depth of 19 km (11 miles). There were no immediate reports of casualties.
Indonesia's Meteorology and Geophysics Agency (BMKG) urged people in a text message to move away from beaches and seek higher ground, noting that the warning applied especially to Seram Island.
BMKG had initially said a tsunami triggered by the movement of tectonic plates was unlikely - but then said one could still be triggered by underwater landslides, of which there would be no warning.
"If the tsunami is caused by an underwater landslide, it cannot be detected from the current early warning system," the head of BMKG, Dwikorita Karnawati,told a news conference.
She said residents should move to higher ground immediately if they felt aftershocks, and not wait for an official alert.
BMKG said in a separate statement that sea levels had risen at one point by as much as 50 cm (20 inches).
It said 13 aftershocks had been recorded so far.
A local civil emergency official said there were no reports of injured people or casualties so far, but some buildings and public facilities had sustained damage.
"Earlier the water level was seen rising briefly, but we have not received further reports yet," said the official, Henri Far Far.
Hundreds of residents ran up hills fearing a tsunami, but then returned home, according to an official with the Central Maluku regency disaster agency.
"Many houses are damaged here," said Asmiathy, a 20-year-old teacher in the area who goes by only one name.
"It’s dark already and everyone here in this village is evacuating to the mountain because we still keep feeling the aftershocks," she said. "I'm still in panic."