He has been criticised for what some regard as anti-Hindu polemic.On 20 March 2000, a few hours before United States President Bill Clinton arrived on his first official visit to India, 38 Sikh villagers were massacred in the village of Chattisinghpura, in the Indian State of Jammu & Kashmir. The killers wore Indian army fatigues. Mishra visited the village hours after the massacre, and later produced a report that was carried by several Indian and international papers. In the report, Mishra amplified Pakistani claims that the Indian army had killed the villagers in an attempt to win U.S. sympathy for the Indian stance on Kashmir. A later report carried by the British newspaper,
The Guardian in July 2002 focused on the allegations of possible abduction and brutal murder by the Indian army of "innocent Kashmiri Muslim civilians" shortly after the massacre.
The massacre coincided with the visit of United States president Bill Clinton to India. In an introduction to a book written by Madeline Albright titled
The Mighty and the Almighty: Reflections on America, God, and World Affairs (2006), he accused "Hindu Militants" of perpetrating the act. The allegation created a major fury, with both Hindu and Sikh groups expressing outrage at the lie. Clinton's office did not return calls seeking comment or clarification. In the hours immediately after the massacre in March 2000, the US condemned the killings but refused, to accept the Indian governments contention that it was the work of Pakistan based Islamist groups. That changed as soon as Clinton's claims were debunked. The publishers, Harper Collins routed a correction through Albrights office. In a public statement they acknowledged the error.
Page xi of the Mighty and the Almighty contains a reference to Hindu militants that will be deleted in subsequent printings, both in America and in international editions.
Mishra's polemics regarding Hinduism as a religion and the modern history of nationalist movements among Hindu people in India such as the Bharatiya Janata Party (BJP) have generated some disquiet mainly among Right wing circles within India. His book
Temptations of the West: How to be Modern in India, Pakistan, Tibet and Beyond was reviewed by
The Economist (1—7 July 2006 issue) and provides an example of the analysis and commentary that have made Mishra controversial in India. His remarks against Hindus have earned him accusations of being an anti-Hindu, and of "pandering to white Anti-Hindu audiences in the West".