The NIA had arrested Meitei in a terror-related case earlier.
"The seized money was deposited in the businessman's account operated in one of the State Bank of India's branch in the city," a NIA source said but declined to name the businessman, as investigation in the terror case was in progress.
The investigation also found that large sums of terror funds made their way into real estate deals in Bangalore.
"This is the largest seizure of cash so far though many moveable and immovable assets were seized in the past under the Unlawful Activities Prevention Act," a NIA statement said.
The NIA had also recorded the unnamed businessman's statement before a magistrate here last week. The cash was seized after a case was registered at its Guwahati branch in Assam.