The vessel was reported to be carrying at least 300 passengers on the Brahmaputra river in Assam state.
Reports say more than 100 people are missing, while dozens of others either were rescued or made it to safety.
Poor safety standards mean ferry accidents are common on the river but that this is one of the worst disasters in recent memory.
Police officials said it happened in the remote district of Dhubri during heavy winds and rain.
Dhubri is about 350 km (215 miles) west of Assam’s main city, Guwahati.
The vessel capsized and broke into two pieces during the storm, police said.
“I could see people being swept away as the river current was very strong,” a witness to the accident, Rahul Karmakar, told AFP news agency.
Assam state Chief Minister Tarun Gogoi said emergency teams were in place but nightfall and bad weather were hampering rescue efforts.
The ferry carried no lifeboats or life jackets, and was overloaded with people and goods, with passengers sitting on the roof, according to a police officer quoted by the Reuters news agency.
In a statement, Indian Prime Minister Manmohan Singh said he was “shocked and grieved” by the incident.
Manmohan Singh has “given instructions for all possible assistance to the government of Assam in relief operations”, the statement added.
Boats are a common mode of transport in the area, which is dotted with small islands and villages along the banks of the river.
Many of the boats are overcrowded with poor or minimal safety features.
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