The agency has registered a case against Roy, his wife Radhika and RRPR Holdings for allegedly causing losses of Rs 48 crore to ICICI Bank, CBI sources told PTI.
The agency was conducting searches in the national capital and Dehradun.
"Searches are being conducted today (Monday) at four places including Delhi and Dehradun," CBI spokesperson R.K. Gaur told IANS.
NDTV termed the move as a "witch-hunt" based on "same old" false accusations.
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"This morning, the CBI stepped up the concerted harassment of NDTV and its promoters based on the same old endless false accusations," NDTV said in a statement.
"NDTV and its promoters will fight tirelessly against this witch-hunt by multiple agencies."
"We will not succumb to these attempts to blatantly undermine democracy and free speech in India. We have one message to those who are trying to destroy the institutions of India and everything it stands for: we will fight for our country and overcome these forces," it said.
Prannoy Roy is the co-founder and executive co-chairperson of New Delhi Television (NDTV) along with his wife Radhika Roy.