Deputy Commissioner Kumud Chandra Kalita said the bodies of 100 victims, including women and children, were recovered by the BSF and the National Disaster Force personnel near Jaleswar.
He said about 25 people swam to safety after the double-decked ferry with over 300 people onboard was crossing the river from Dhubrighat when it capsized in the storm at 4.20 pm. The bodies of the victims were kept at the Dhubri civil hospital, he said, adding the fate of the remaining passengers was not immediately known.
The steamer had left Dhubri ferry ghat for Medartary in south bank of the district in the evening and capsized because of the impact of the storm.
The Army, BSF's water wing, National Disaster Force and police armed with mechanised boats have launched a massive rescue operation in the river but darkness, bad weather and strong current hampered search for possible survivors or the dead.
President Pratibha Patil expressed grief over the loss of life while Prime Minister Manmohan Singh assured the state government of all help for relief and fund for families of the deceased.
Dr Singh spoke to Chief Minister Tarun Gogoi to convey his condolences. Mr Gogoi has ordered an inquiry and asked the district administration to look after the survivors.
In another boat capsize, 12 people were missing when a boat sank in the same river at Jaleswar, officials said.
The district administration has issued a red alert in view of the storm.
"The storm has resulted in the tragedies and we are taking all measures," Mr Kalita said.