Hemanta Kumar Bordoloi, a teacher of Nabheti Madhya Ingraji school, went missing from his home three days ago.
His body was found floating in a pond at Nabheti area by the police.
Bordoloi was employed in the government-aided middle school but was upset as he did not receive the salary for the past 18 years, his family members alleged.
The school was included under the Right to Education Act but its teachers were yet to get their salary from the state's education department.