Commissioner Jishnu Barua of Assam state in northeastern India told CNN early Tuesday that 90 people were rescued and 40 bodies had been recovered so far.
Barua said the ferry apparently broke apart as it was about to dock after a storm Monday night.
He said it was carrying approximately 300 passengers at the time, more than its stated capacity of 280.
Local officials told the Hindustan Times there may have been as many as 500 people on board.
Passenger Taleb Ali, 42, told the Times he was able to swim to shore and to help at least four others survive.
"Overloading is normal in these parts," Ali said. "There were at least 500 people on the boat, and I was lucky to have been on the upper deck. Most of the people were in the cage-like lower deck and I fear they were trapped. The death toll will cross 200."
Pradip Kumar, the police chief in Dhubri, said the ferry was en route from Dhubri on a 3-hour trip southeast to Hatsinghimari when it ran into the cyclonic storm.