Thounaojam Herojit flew from Delhi on Wednesday afternoon. But he never came out of the airport, disappointing journalists waiting for him outside the main exit.
Officials confirmed that Herojit was on the plane but could not say where he had gone.
The development comes shortly after Home Minister Rajnath Singh promised action on Herojit's claim over the killing of the ex-insurgent, Chungkham Sanjit.
A former insurgent, Sanjit had given up militancy. He was allegedly trapped inside a chemist's shop on B.T. Road in Imphal, and a few minutes later his body was dragged out by security personnel.
Police told the media that he was killed in an exchange of fire. The CBI, which probed the case after public outcry, however accused Head Constable Herojit of killing Sanjit.
Herojit later said he committed the killing on the orders of a senior officer.
According to rights activists, there are 1,528 known cases of 'fake encounters' in Manipur since the beginning of the insurgency in the late 1970s.
The Supreme Court is looking into the alleged 'fake encounters'.
If cases of "missing persons" are taken into account, the number will be more, the activists say.