Clarkson, one of the highest paid BBC presenters known for his controversial comments, presented the Top Gear programme, which since its broadcast prompted several complaints and allegations of racism.
In its January 6 letter to the programme's producer, Chris Hale, and copied to Mark Thompson, director-general of BBC, the high commission said the BBC was "clearly in breach of the agreement that you had entered into, completely negating our constructive and proactive facilitation".
The letter added: "The programme was replete with cheap jibes, tasteless humour and lacked cultural sensitivity. This is not clearly what we expect of the BBC. I write this to convey our deep disappointment over the documentary for its content and the tone of the presentation".
In the programme, Clarkson allegedly made controversial comments about India's trains, toilets, clothing, food and history.
The BBC has confirmed receiving 23 complaints about the programme, and added that it would directly respond to the Indian high commission's letter.
Senior Labour MP Keith Vaz, who called for a BBC apology when the programme was broadcast over Christmas, told The Telegraph last night: "It seems that the reasons given by the BBC in order to obtain their visas to go to India did not disclose the true nature of the content of this programme."