Bombay residents were ordered to stay home for the second day in a row as heavy rains that began late on Sunday pounded western Maharashtra state.
Navy divers were deployed in low-lying areas to ferry marooned people to safety as floodwaters entered homes in the worst affected areas in Bombay's northern suburbs and other parts of the inundated state.
"The toll is expected to cross 1000," K Vatsa, Maharashtra's rehabilitation secretary, said on Monday.
As many as 421 people were killed in Bombay.
Most deaths were caused by landslides and flooding after a record 94cm fell last Tuesday over 24 hours, cutting off the state from the rest of the country.
Schools and colleges remained closed on Monday and streets were deserted.
Most deaths were caused by
landslides and flooding
Usually crowded commuter trains were mostly empty, and rail authorities were monitoring the situation as renewed flooding threatened to submerge tracks.
"Trains are running, but they are running late. If the rains continue to be so heavy, we will have to stop (services)," said railway spokesman Shailendra Kumar. He added that long-distance train travel had been cancelled.
Bombay's two main airports were open, but few flights were operating.
Health workers were deployed in Bombay's suburbs to distribute medicine and disinfectants to guard against the spread of waterborne disease.
"We didn't sleep the whole night seeing the water level rise," said Shakuntala Nath, 68, standing outside her water-filled shanty home in Santa Cruz district.
Health workers are distributing
medicine and disinfectants
"Everything is wet; our beds, furniture, all our belongings. When will this stop?"
Electricity was gradually being restored to many neighbourhoods after angry residents demonstrated on Saturday demanding the restoration of tap water, power and the cleanup of garbage and decomposing animal carcasses.
About 25,000 sheep and goats and 2500 buffaloes drowned in Bombay, officials said.