The company refuted the allegations and accused the CBI of "concerted harassment of NDTV and its promoters based on the same old endless false accusations".
"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," NDTV said in a statement.
The investigation comes at a time of often heated, polarising debate in India's fiercely competitive TV news industry, where channels sometimes test the boundaries of responsible journalism and prime-time talk shows are often rowdy and contentious.
Police conducted raids at Roy's residence in New Delhi and at two vacation homes.
Neither of the couple were available for comment but NDTV presenter Srinivasan Jain said the "message is clear".
"Any independent voices in media will be bullied and shut down. Black day," tweeted Jain.
The CBI said the investigation had no link to the editorial line of NDTV, India's oldest English-language all-news channel.
"We have nothing against NDTV's news coverage ... they are accused of a financial fraud and it's our duty to investigate," a senior CBI official said.
India slipped by three places to 136th in this year's World Press Freedom Index compiled by Reporters Without Borders, which highlighted concerns that Hindu nationalists were "trying to purge all manifestations of anti-national thought".
Senior officials in Prime Minister Narendra Modi's office and members of his nationalist BJP have told Reuters they consider NDTV to be the least-government friendly channel.
In a heated exchange last Thursday, an NDTV moderator demanded that a spokesman of the ruling Bharatiya Janata Party (BJP) either apologise or leave their live debate after he accused the channel of pursuing an anti-government agenda.