The BBC will not be put off from reporting without fear or favour, its Director-General Tim Davie has said in an email to staff in India.
It follows searches at BBC offices in Delhi and Mumbai by tax officials.
Mr Davie thanked staff for their courage and said nothing was more important than reporting impartially.
The BBC, which is co-operating with the investigation, recently aired a documentary critical of Indian Prime Minister Narendra Modi.
India’s government called it “hostile propaganda” and attempted to block it being aired domestically.
Mr Davie said the BBC would help staff do their jobs effectively and safely.
“Nothing is more important than our ability to report without fear or favour,” he said in the email.
“Our duty to our audiences around the world is to pursue the facts through independent and impartial journalism, and to produce and distribute the very best creative content. We won’t be put off from that task.
“I’d like to be clear: the BBC does not have an agenda – we are driven by purpose. And our first public purpose is to provide impartial news and information to help people understand and engage with the world around them.”
Tax officials spent three days carrying out what they called a “survey” at the BBC offices.
India’s Central Board of Direct Taxes said it had found “discrepancies and inconsistencies” as well as evidence indicating “that tax has not been paid on certain remittances which have not been disclosed as income in India by the foreign entities of the group”.
Earlier this week opposition MPs in the UK described the raids as “intimidation” and deeply worrying.
A Foreign Office minister would not comment on the allegations by India’s income tax department but said “we continue to follow the matter closely”.