The girls, students of Class IX and X, were missing since Wednesday and were traced in the shocking state after their relatives launched a frantic search.
Local people said the two girls were raped, murdered and hanged from the tree.
The bodies of the two girls in Assam were sent for post-mortem to a hospital in Silchar, police said. No arrests had been made till the last reports came in. The security was hightened in the area.
In May, two Dalit sisters were found hanging from a mango tree in Badaun district of Uttar Pradesh.