Indian federal authorities launched a fraud investigation on Monday into the founders of news channel NDTV, a move the company said was an attempt to muzzle free speech.

Two top officials said the Central Bureau of Investigation (CBI) had brought a case against NDTV founders, Prannoy and Radhika Roy, over a multi-million-dollar loan, and police raided the couple's New Delhi home as well as two holiday houses.

The company refuted allegations that the bank loan was unpaid 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," an NDTV statement said.

The investigation comes at a time of polarising debate in India's fiercely competitive TV news industry, where channels sometimes test the boundaries of responsible journalism and prime-time talk shows often turn rowdy.

Neither of the Roys were available for comment but NDTV presenter Sreenivasan Jain said the "message is clear".

"Any independent voices in media will be bullied and shut down. Black day," he tweeted.

Late on Monday, NDTV posted a document on its website that it said proved the loan in question, worth 480 million rupees ($7.45 million) was repaid more than seven years ago.

"It is clearly the independence and fearlessness of NDTV's team that the ruling party's politicians cannot stomach and the CBI raid is merely another attempt at silencing the media," the company said in an updated statement.

The CBI said the investigation had no link to the editorial side 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," one of the two senior CBI officials said.

India slipped 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 Bharatiya Janata Party (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 BJP spokesman either apologise or leave a live debate after he said the channel was pursuing an anti-government agenda.