This is the third quake felt in Sabah since Thursday.
The number of people evacuated is expected to rise from 129 recorded this morning.
It advises public to get authentic information from its website instead of believing viral messages spread over WhatsApp.
Putrajaya expresses condolences to family members of victims killed in the quake.
The casualties and damage occurred at Persisir Selatan district in Sumatra.
More than 80 people in the country were injured, mostly in stampedes as panicked residents fled their homes and offices.