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The searches are underway in Aizawl, Imphal and Gurgaon, the officials said.
It is alleged that O Ibobi Singh, the then chairman of the Manipur Development Society (MDS), had conspired with others during his tenure from June 2009-July 2017 and misappropriated government funds worth approximately Rs 332 crore out of Rs 518 crore that was entrusted to them for the purpose of executing development work, according to the officials.
The CBI has registered the case on the request of the Manipur government, which was routed through the Centre.