Home Ministry (MHA) has asked the National Investigation Agency (NIA) to probe the assassination of social activist Athuan Abonmai.
The decision from the centre came after state police chief LM Khaute proposal for a higher-level probe in the matter, Manipur's Special Secretary (Home) H Gyan Prakash said.
The Manipur police chief had earlier constituted a team headed by senior state police official Radhashyam Singh, with two other top ranked officials K Kabib and Kamei Angam Romanus to probe the case.
Meanwhile, the Manipur government has suspended 16 policemen, including some troopers of Manipur Rifles over the killing.
Athuan Abonmai was shot dead soon after he was kidnapped by armed men on September 22 in state's Tamenglong district.
The policemen allegedly behaved as mere onlookers while Abonmai was being dragged out and bundled into a waiting jeep.
After the widespread condemnation, Manipur chief minister N Biren Singh had publicly apologized for the police inaction during the incident.
"I wondered how the morale of the police had lowered to such an extent. Police should have taken swift action and saved the life of Abonmai," Mr Singh, who also holds the home portfolio, had said.
Athuan Abonmai was abducted on September 22 when the Chief Minister, accompanied by his ministerial colleagues, visited the Tamelong district bordering Assam and Nagaland to inaugurate some projects.
The tribal leader was reportedly abducted while he was on his way to attend the Chief Minister's programme.
According to reports, 20 armed members allegedly from NSCN (IM), kidnapped Abonmai near Pallong village.
Police are yet to ascertain the motive behind the incident with no group claiming responsibility for the kidnapping and killing of the tribal leader.
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