"Shoot-on-sight orders have been issued and curfew has been imposed in the violence-hit areas," Tarun Gogoi, Assam's chief minister, said.
Others were burned to death when attackers set fire to homes belonging to members of the rival community, police said.
More than one dozen people have been admitted to hospital in Guwahati, Assam's main city, with serious burns.
Police and paramilitary troops opened fire in at least three separate locations in an attempt to stop arson attacks, officials said.
More than 400 homes have been torched and at least 30,000 people have fled their villages in an area which is partly controlled by the Bodo as part of a deal that saw many of the tribal people abandon claims for an independent homeland.
"The picture is hazy and compilation of casualty figures has become difficult because of the continuing arson," Himanta Biswa Sarma, a state government spokesman, said. "We are mobilising all resources to control the situation."
An indefinite curfew has been imposed in the northern districts of Assam and army and paramilitary forces have been brought in to restore calm.
The Bodos and Muslim immigrants have clashed sporadically over land disputes in the region. Throughout the 1990s, at least 250 people were killed and an estimated 300,000 displaced as a result of the violence.
Northeast India is home to more than 200 tribes and has seen a number of violent uprisings by groups demanding autonomy since the country gained independence from Britain in 1947.