Speaking at the ongoing Jaipur Literature Festival, the 61-year-old Member of Parliament said there was a dire need for Hindus to stand up and recognise what was being done "in their name" and speak out against it.
"We need to call a spade a spade. We are living in a country where on the one hand the prime minister says the Constitution is his holy book and on the other hand he extols as a hero and instructs his ministries to study the works, writings and teachings of Deen Dayal Upadhyay, who explicitly rejects the Constitution and who shares that the Constitution is fundamentally flawed," the former Union minister said.
The two thoughts, he said, were contradictory.
"You can't have these two thoughts in the same sentence... To have it both and to be allowed by our public discourse to get away with it for so long seems to me somewhat troubling," he said to thunderous applause from the audience at the packed front lawn, the largest venue at the iconic Diggi Palace where the festival is being held.
Mr Tharoor said Upadhyay believed the Constitution "rests on the flawed premise that the nation is a territory of India and all the people on it".
"Whereas he (Upadhyay) says that is not correct, the nation is not a territory, it is a people and it is therefore the Hindu people. Which means you need a Hindu nation, a Hindu rashtra and that is what the Constitution should reflect, which of course it does not," he said.
That, Mr Tharoor added, was the essential contradiction. "(You) cannot hail Upadhyay and the Constitution ... at the same time," he said.
The Thiruvananthapuram Member of Parliament described himself as a "devotee" of Swami Vivekananda's teachings, and said the acceptance of differences was at the heart of Hinduism.
"Hinduism is not a faith of absolute certitudes... How such a wonderfully capacious faith so open, so classically liberal in that sense can be reduced by some into a badge of identity akin to that of a British hooligan, reducing our wonderful metaphysics to a chauvinistic rampage, I don't know," he said.
The time had come, he said, to take Hinduism back to the "real" Hindus.
"There are a lot of people going around expressing thoughts, condoning actions in the name of Hinduism that most Hindus starting with the likes of Swami Vivekananda would not recognise," he said.
Mr Tharoor, who has written 16 books, was in conversation with poet Arundhati Subramaniam, and talked about his new book, 'Why I Am a Hindu'.
He said Hinduism was totally compatible with a modern, liberal and pluralistic society and was in many ways almost the "perfect" religion of the 21st century.
"It is being reduced and traduced into something that it is not. We need to have a serious taking back of Hinduism and facing up to what it teaches because very often the alternatives that are being taught are actually dangerous to our social peace and cohesion," he said.
Some people were not only willing to "advertise their Hinduism", but claimed that it was the only possible way of being a Hindu, he said.
"This is a sort of Hindu wahabism... It is high time that for those of us who believe that we are good Hindus, that we take back our faith from these people who portray it that way and that is what this book seeks to do," Mr Tharoor said.
He said a great deal can be learnt from the mahatmas of the past, noting that it was not only their teachings but also their lives that offer lessons for today's Hindus.
"If indeed people are willing to immolate themselves over a film that they have never seen or burn buses and attack school children to protest somebody else's freedom of expression then there is something wrong with our society and we have to understand that answers need to be found," Mr Tharoor said.
These people, he added, were "anti-Hindus".
"Instead of punishing themselves which the likes of Gandhi and Vivekananda would have approved of, the people are going around punishing others, attack others, write against others, lynch others. They are the anti-Hindus," he said.