The BBC said it was fully cooperating with the Income Tax surveys.
The News Broadcasters and Digital Association (NBDA) has expressed "deep anguish" over the Income Tax surveys conducted at the offices of BBC, a member of the media group.
"While NBDA maintains that no institution is above the law, it condemns any attempt to muzzle and intimidate the media and interfere with the free functioning of journalists and media organisations. Such attempts undermine the basic tenets of free speech as enshrined in the constitution and severely affect the free and fearless functioning of a democracy," the NBDA said in a statement.
"NBDA states that such Income Tax 'surveys' leads to consistent harassment of the media, which also impacts the reputation and image of India as the world's largest democracy. NBDA urges the Government to ensure that any investigation undertaken by it, must be in strict adherence with the principles of natural justice and the prevalent law," it added.
Income Tax officials searched the BBC's Delhi and Mumbai offices on Tuesday, weeks after a massive controversy over the UK national broadcaster's documentary on Prime Minister Narendra Modi and the deadly sectarian riots in Gujarat in 2002.
The taxmen sealed off the offices for a "survey" linked to alleged diversion of profits and irregularities in transfer pricing involving the BBC. Sources say, the Income Tax authorities are checking account details dating as far back as 2012.
"The Income Tax Authorities are currently at the BBC offices in New Delhi and Mumbai and we are fully cooperating. We hope to have this situation resolved as soon as possible," the BBC tweeted.
The opposition accused the government of targeting the BBC for airing a documentary critical of PM Modi over the riots that swept Gujarat in 2002, when he was Chief Minister. The Editors Guild of India said the raids were part of a wider "trend of using government agencies to intimidate or harass press organisations that are critical of government policies".
The two-part series, "India: The Modi Question", was taken down from public platforms last month. The Centre used emergency powers under IT Rules to block YouTube videos and Twitter posts sharing links to the documentary. The government slammed the documentary as "hostile propaganda and anti-India garbage".