The body of the jawan was found floating in the small pond located within the complex in the Khabeisoi area, a police official said.
The jawan hailed from Churachandpur district of Manipur.
Though the exact cause of the death is not known, drowning could be a possibility, he said.
Earlier on June 22 last, two persons -- a surrendered militant and his driver -- were found shot dead at the same base and the responsibility for the killing was claimed by the Red Army of the proscribed outfit PREPAK.