Flooding caused by high tides is threatening many low-lying areas of the Andaman and Nicobar archipelago, including the capital, Port Blair.
Many survivors are in camps in Port Blair
Port officials say water levels across the islands are several feet higher than in normal high tides.
There is speculation that the sea bed in the area may have risen after the December tsunami, making flooding more common and cultivation more difficult.
India's death toll is now 10,136, with 5,630 still missing, feared dead.
Thousands of people have been moving to higher ground as waves crashed over sea walls in Port Blair.
High tide on Monday was scheduled to peak at 2.35 metres, 10 centimetres higher than Sunday's levels when low-lying areas were flooded.
The authorities say all inhabited islands have been visited
"Yesterday's water destroyed our belongings so we are not taking chances today as the tide level is expected to be even higher," Varun Singh, a resident of the seaside district of Corbyn's Cove, told the AFP news agency.
The BBC's Subir Bhaumik in Port Blair says that these are the first peak high tides there since the tsunami disaster.
Hydrographers have warned that if the islands continue to be inundated by high tides, many coastal areas may become uninhabitable.
ANDAMAN AND NICOBAR
About 400 islands, 38 inhabited
Islands are peaks of submerged mountain range
Indian territory, area of 8,249 sq km
Population around 370,000, about 100,000 in Port Blair
Number of tribes, including Jarawas, Onges and Shompens
Indian Prime Minister Manmohan Singh has promised to set up a scientific committee to assess tidal and seismic patterns and assess which areas of the islands are habitable and which are not.
During a visit to the Andaman and Nicobar islands on Saturday, he also announced a grant of $40m for immediate relief work. The disaster in the archipelago has left more than 1,300 people dead, 5,544 people missing and some 55,000 others displaced.
It has also destroyed villages and created piles of debris that threaten mangrove forests and coral reefs.
"There will be a large amount of changes - in the life support systems of the tribals, in the forests, in crops, in the animals and birds," environmentalist Samir Acharya told the Associated Press news agency.