The Home Ministry has issued a notification formally handing over the case to the NIA, which will immediately start the investigation, official sources said.
The NIA, which was set up after the 2008 Mumbai terror attack, is mandated to probe all terror related cases anywhere in the country.
"Since the Manipur incident is one of the worst cases in the recent past, the Centre has promptly decided to hand over the case to the central investigating agency," sources said.
In the worst such attack in two decades, insurgents on Thursday ambushed a military convoy in Manipur's Chandel district killing at least 18 army personnel and injuring 11 others.
Army Chief General Dalbir Singh Suhag went to Manipur on Friday as security forces intensified their operations in the state following the deadly ambush.
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