"Every single one of these so called valorous maharajas, who today are after a Mumbai filmmaker because their honour is at stake, they were less concerned about their honour when the British were trampling all over it. They scurried to accommodate themselves," said Mr Tharoor during an event in Mumbai.
The remarks come at a time when groups like the Shri Karni Sena have increased their threats to the makers of the film 'Padmavati', leading to the Maharashtra government giving security to Sanjay Leela Bhansali, the film's director.
A Karni Sena leader had also allegedly said that the Sena would do to the film's lead actor Deepika Padukone "what Lakshman did to Shurpanakha," referring to the act of cutting off the mythological figure's nose.
When asked that his book had claimed victimhood, inspite of saying the Maharajas worked with the British instead of against them, the Congress leader never claimed to do so.
"It is (our fault) and I say so. I actually don't take the mantle of victimhood. In about half a dozen places in the book, I am harsh enough on us... Some British reviewers said 'Why doesn't he explain why the British conquered?' And it's a fair question...," Mr Tharoor said.
Mr Tharoor also said Mahatma Gandhi had been capable of showing to the British, their own heinous acts as former colonists.
However, faced with anger online, he issued a clarification on Twitter.
"I am dismayed that some BJP supporters are claiming I attacked Rajput honour... I spoke about the Maharajahs who made their accommodations with the British. I have never made a communal comment in my life," he said.
"As for specific concerns of the Rajput community, people's sentiments must be respected in the interests of India's diversity and harmony. Rajput valour is part of our history and is not in question. BJP and its censors should take these concerns into account," he added.
(With Inputs From PTI)