Gorontalo area of Sulawesi island was struck with a magnitude 7.7 quake at a depth of 6.2 miles, the agency has said.
Afterwards, another second quake struck 6.0 magnitude in northern Sulawesi.
Indonesia launched a hi-tech system on Tuesday to detect a forthcoming tsunami.
Some 17,000 islands lies in the ‘Pacific Ring of Fire’.
The place was hit by a strong and destructive tsunami four years ago which killed thousands and many were missing.