In Karnataka, several structures at world heritage site Hampi, an ancient town, were flooded.
So far 60 people have died in rain-related incidents, said state chief minister B S Yediyurappa, adding nearly 227,000 people were staying in relief camps.
While Karnataka, Kerala and Maharashtra have been the worst hit this year, several other states including Gujarat, Assam and Bihar have also seen heavy damage due to floods.
In Maharashtra, where the death toll stood at 30, the flood situation was improving, according to state-run All India Radio, though authorities said it would be difficult to restore rail services in some flood-hit areas within the next two weeks.
India's main opposition Congress party called on Prime Minister Narendra Modi to provide relief packages.
Citing media reports, the Congress party said so far this year 446 people have been killed in six flood-hit states including Assam, Bihar and Gujarat.
"Despite the mammoth loss of lives and displacement caused due to floods, the government is failing to realise the gravity of the flood fury," the Congress party said in a statement on Sunday.
Reuters