Eight leaders of the United Liberation Front of Asom met with Home Minister Palaniappan Chidambaram and then began talks with Home Secretary G.K. Pillai.
The peace talks became possible after the government released seven rebel leaders, including chairman Arabinda Rajkhowa, from prison in Assam state. The government also offered them safe passage to facilitate the talks.
The rebel leaders face sedition charges, punishable by life imprisonment.
The separatists accuse the Indian government of exploiting Assam state's natural resources while doing little for the indigenous people, most of whom are ethnically closer to the people of Myanmar and China than to other Indians.
"We want to resolve the conflict through political dialogue," Sasha Chowdhary, a rebel leader, told reporters.
Chidambaram said he told the rebels he was confident the talks could lead to a just and honorable solution.
However, the talks have revealed a split in the rebel ranks. Paresh Barua, the group's commander in chief, and his supporters oppose peace talks and are continuing to demand an independent state. Other rebel leaders have joined hands with chairman Arabinda Rajkhowa in pursuit of a negotiated peace.
More than 30 groups in the northeast have been fighting for decades for independence or wide autonomy in the region, about 1,000 miles (1,600 kilometers) east of New Delhi.