The monsoon floods have inundated at least 17 districts in Assam and affected over four lakh people, officials said. The Brahmaputra, one of the world's largest rivers that cuts through Guwahati, and five other rivers are flowing above the danger mark, officials said.
Ferry services across Assam have been stopped after the weather office forecast more rain.
In neighbouring Arunachal Pradesh, two school children died after they got buried in a landslide in Tawang, close to the border with China, taking the number of dead to six since Tuesday when heavy rain started in the region.
Dhemaji and Lakhimpur in the tea-rich Upper Assam, and Bongaigaon and Barpeta in Lower Assam are the worst hit.
Officials said floodwaters from the higher areas will flow towards the valleys, worsening the situation in Lower Assam areas.
Bhutan has also issued a flood warning for areas in the foothills.
Among the 17 districts, Barpeta is the worst-affected with over 85,000 people seeking shelter, said the Assam State Disaster Management Authority.
Flood waters have entered the Kaziranga National Park in Upper Assam,home to the endangered one-horned rhinoceros species, forcing the animals to take shelter on platforms constructed for their safety,officials said.
The Assam Chief Minister, Mr. Sarbananda Sonowal, spoke with the deputy commissioners of the affected districts to assess the situation. He directed them to set up round-the-clock control rooms and respond to people's calls for help during emergency.
Amid the flood, Assam is also grappling with rising cases of encephalitis and the state government has cancelled the leaves of all health department employees till the end of September to deal with the outbreak.
Nine districts in Assam are most vulnerable to encephalitis. Since 2013, over 700 people have died of the disease.