The searches in New Delhi and Mumbai come weeks after the broadcaster aired a documentary in the UK critical of Indian Prime Minister Narendra Modi.
The BBC said that it was “fully co-operating” with authorities.
“We hope to have this situation resolved as soon as possible,” a short statement added.
Although the documentary was broadcast on television only in the UK, India’s government has attempted to block people sharing India: The Modi Question online, calling it “hostile propaganda and anti-India garbage” with a “colonial mind-set”.
Last month, police in Delhi detained students as they gathered to watch the film.
The documentary focused on the prime minister’s role in anti-Muslim violence in Gujarat in 2002, when he was chief minister of the state.
The general secretary of the opposition Congress party, KC Venugopal, said Tuesday’s search “reeks of desperation and shows that the Modi government is scared of criticism”.
“We condemn these intimidation tactics in the harshest terms. This undemocratic and dictatorial attitude cannot go on any longer,” he tweeted.
But Gaurav Bhatia, a spokesman from Mr Modi’s ruling Bharatiya Janata Party (BJP), described the BBC as the “most corrupt organisation in the world”.
“India is a country which gives an opportunity to every organisation,” he said, “as long as you don’t spew venom.”
He added the searches were lawful and the timing had nothing to do with the government.
The Editors Guild of India – a non-profit group which promotes press freedom – said it was “deeply concerned” about the searches.
They are a “continuation of a trend of using government agencies to intimidate and harass press organisations that are critical of government policies or the ruling establishment”, it said.
Amnesty International India’s Board accused authorities of “trying to harass and intimidate the BBC over its critical coverage of the ruling Bharatiya Janata Party”.
It said the “overbroad powers of the Income Tax Department are repeatedly being weaponised to silence dissent”.
The documentary highlights a previously unpublished report, obtained by the BBC from the UK Foreign Office, which raises questions about Mr Modi’s actions during the 2002 riots.
The rioting began the day after a train carrying Hindu pilgrims was set on fire, killing dozens. More than 1,000 people, mostly Muslims, died in the subsequent violence.
The Foreign Office report claims that Mr Modi was “directly responsible” for the “climate of impunity” that enabled the violence.
In 2005, the US denied Mr Modi a visa under a law that bars the entry of foreign officials seen to be responsible for “severe violations of religious freedom”.
Mr Modi has long rejected accusations against him, and has not apologised for the riots. In 2013, a Supreme Court panel also said there was insufficient evidence to prosecute him.
The BBC said last month that the Indian government was offered a right to reply to the documentary but it declined.
The broadcaster said the film was “rigorously researched” and “a wide range of voices, witnesses and experts were approached, and we have featured a range of opinions, including responses from people in the BJP”.
Source: BBC
