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Government authorities said 50 people were missing.
Japan's weather agency said several small tsunami waves reached parts of the southern prefecture of Okinawa.
Kerala State Disaster Management Authority assured that there is no need to panic.
The Kerala and south Tamil Nadu coasts are likely to witness 0.5 to 1.5 metre high waves and storm surge till 11.30 pm.
Fishing boats are stranded due to the receding sea, with fishermen observing unusual tidal activity.
The disaster left more than 30,000 people homeless and cut power to tens of thousands of residences and businesses.
Survival rates drop off 72 hours after the quake, according to emergency responders. Severed roads and the remote location of the worst-hit areas have complicated rescue efforts.
Around 200 tremors have been detected since the quake first hit on Monday, according to the Japan Meteorological Agency, which warned that more strong shocks could hit in the coming days.
The quake with a preliminary magnitude of 7.6 triggered waves of around 1 metre along parts of the Sea of Japan coast with a larger wave expected, public broadcaster NHK reported.
Evacuation orders were issued for some areas in the Philippines and southwestern Japanese coasts because of warnings of tsunami waves of a metre (3 feet) or more.
