Further tsunami warnings were later lifted.
The earthquake was 30km under the seabed, its epicentre 234km northwest of Ternate, the capital of North Maluku.
The quake came as other regions of Indonesia were struggling to cope in the aftermath of widespread flooding and a series of landslides.
The US National Weather Service said on Thursday that there was no threat of a destructive, widespread tsunami.
Indonesia was worst hit by the 2004 Indian Ocean tsunami, which killed 168,000 people in Aceh province.
Rescuers say further flooding and landslides on Sulawesi Island have restricted the supply of food and aid to 20,000 people forced out of their homes.
About 40 people are thought to be buried under the mud in Central Sulawesi, but the weather and lack of heavy equipment has hampered rescue efforts.
Days of heavy rain have brought landslides and floods up to three metres high. Hundreds of homes are submerged and at least 60 people are dead.
Frets Abast, who is co-ordinating provincial disaster relief, said the floods had spread to two more districts.
In North Sulawesi province, 15,000 people found their homes inundated after Wednesday's flooding, killing one person and injuring 17.
In neighbouring South Sulawesi, a landslide killed nine in a remote village on Tuesday night.
Pakaya said Jakarta had sent health teams with food and medicines, but heavy rain had made access to the affected areas difficult and stopped helicopter food drops.
A navy warship carrying food, tents and blanket is scheduled to arrive on Thursday.
Deadly landslides occur frequently in Indonesia, where tropical downpours can soak hillsides stripped of trees with little vegetation to hold the soil.
Central Sulawesi is also one of Indonesia's cocoa growing areas. The Southeast Asian country is the world's third-largest producer of cocoa beans.