One high profile critic of Thapar is journalist, politician, and writer Arun Shourie, whose book Eminent Historians: Their Technology, Their Line, Their Fraud accuses her and other historians of white-washing the records of Muslim rulers such as Mahmud of Ghazni and Aurangzeb and of tampering with history.
She crtisized Hindus for objecting to Hussains painting, but said nothing about the intolerance of Muslims towards Cartoon. These kind of hypocrasy lends credence to her being called biased.
Thapar is critical of what she calls a "communal interpretation" of Indian history, in which events in the last thousand years are interpreted solely in terms of a notional continual conflict between monolithic Hindu and Muslim communities. Thapar says this communal history is "extremely selective" in choosing facts, "deliberately partisan" in interpretation and does not follow current methods of analysis using multiple, prioritised causes.
In 2002, the Indian coalition government led by the Bharatiya Janata Party (BJP) changed the school textbooks for social sciences and history, on the ground that certain passages offended the sensibilities of some religious and caste groups. Romila Thapar, who was the author of the textbook on Ancient India for class VI, objected to the changes made without her permission that, for example, deleted passages on eating of beef in ancient times, and the formulation of the caste system. She questioned whether the changes were an, "attempt to replace mainstream history with a Hindutva version of history", with the view to use the resultant controversy as "election propaganda." Other historians and commentators, including Bipan Chandra, Sumit Sarkar, Irfan Habib, R.S. Sharma, Vir Sanghvi, Dileep Padgaonkar and Amartya Sen also protested the changes and published their objections in a compilation titled, Communalisation of Education.
Writing about the 2006 Californian Hindu textbook controversy, Thapar opposed some of the changes that were proposed by Hindu groups to the coverage of Hinduism and Indian history in school textbooks. She contended that while Hindus have a legitimate right to a fair and culturally sensitive representation, some of the proposed changes included material that pushed political agenda.
Thapar's appointment to the Library of Congress's Kluge Chair in 2003 was opposed in an online petition bearing more than 2,000 signatures, on the grounds that she was a "Marxist and anti-Hindu" and it was "waste of US money" to support a leftist. Journalist Praful Bidwai criticised the petition as a "vicious attack" by communalists who are "not even minimally acquainted" with her work. A number of academics sent a protest letter to the Library of Congress denouncing the petition as an attack on intellectual and artistic freedom. The Communist Party of India (Marxist) supported her appointment by calling her "a liberal with a scientific outlook". Martha Nussbaum has stated that Thapar is neither a communist nor a Marxist historian and the Library of Congress treated the petition with "the indifference that it deserved".
"Taliban did not destroy the statue of Buddha at all. There was no historical evidence to prove that those statues were of Buddha".
"There is in reality no such thing as Hinduism".
"Islamic invaders' motive was economic rather than religious".
"Hinduism was invented during the nineteenth century as a response to British colonial rule".
“Aurangzeb’s supposed intolerance is little more than a hostile legend based on isolated acts such as the erection of a mosque on a temple site in Benares.”
“…Young boys stayed with the priests who taught them how to recite the hymns of the Vedas. There is an amusing description of the pupils in one of the hymns. It is said that the pupils repeating the lesson after the teacher sound like frogs croaking before the coming of the rains.”
"Jadunath Sarkar, R.C. Majumdar and K.S. Lal are examples of communalist and colonialist historywriting in textbooks".
"The insistence on the tradition of religious tolerance and non-violence as characteristic of Hinduism... is not borne out by historical evidence".
Criticism of Romila Thapar
- Romila Thapars Ancient India, A Textbook of History for Middle Schools
- Appointment of Professor Romila Thapar to the Kluge Chair at the Library of Congress, Washington, D.C.
- It is Official Now - Romila Thapar Defends the Aryan Invasion Theory!
- Harsha of Kashmir A Hindu Iconoclast? by Koenraad Elst http://koenraadelst.bharatvani.org/articles/ayodhya/harshakashmir.html
- India - Another Millennium? by Sanjay Garg http://bharatvani.org/indology/millennium.html
- Prof. Thapar and the Kluge Chair - An Open letter of protest to the LOC; http://bharatvani.org/indology/klugethapar.html
- [For a Word version (slightly different), click here] ; [PDF] by Vishal Agarwal http://bharatvani.org/indology.html
- Questionnaire for the Marxist Professors (Appendix IV of Hindu Temples, What Happened to Them, Vol. II) by Sita Ram Goel http://bharatvani.org/books/htemples2/app4.htm
- Review of Ancient India, Class VI NCERT History Textbook (MS Word). [For PDF version, click here] by Vishal Agarwal http://vishalagarwal.bharatvani.org/articles/indhistory/misrep.htm
- Review of "Medieval India", Class VII NCERT History Textbook by M. Pramod Kumar http://www.bharatvani.org/indology/thaparreview1.html
- A Review of Romila Thapar's Early India (2002, 2003) ; [MS-WORD ; PDF ] by Kalavai Venkat http://bharatvani.org/indology/EarlyIndia.html
- Review of Romila Thapar's Somanatha, The Many Voices of a History(Penguin 2004), by Meenakshi Jain http://bharatvani.org/indology/somnath.html
- The autobiography of K.K. Muhammed (about her role in the Ayodhya debate)
- Diluting the record of Islam – Dilip Kumar Charkrabarti
- 'A Dictionary of The Marxist Thought' (Tom Bottomore et al, 1983, Harvard University Press, p. 204, entry "Hinduism"). Ronald Inden: Imagining India [1990:pp. 154-156, 197] See also Appendix C: Dossier on Romila Thapar
- Thapar, Jha and Sharma are quoted Marxist historians in the entry 'Hinduism' of 'A Dictionary of The Marxist Thought' (Tom BOTTOMORE et al, 1983, Harvard University Press, p. 204). Ronald INDEN, in his Imagining India [1990:pp. 154-156, 197] clearly refers to Thapar as a Marxist historian. According to Witzels characterizations, Inden and Bottomore would also be "Right Wing Hindu Fundamentalists" 
- "The Rediff Interview/ Romila Thapar". Rediff. 4 February 1999.
- Chaudhry, D.R. (28 April 2002). "Critiques galore!". The Tribune. Retrieved 7 April 2009.
- "Hating Romila Thapar". 2003. Retrieved 3 September 2014.
- Mukherji, Mridula; Mukherji, Aditya, eds. (2002). Communalisation of Education: The history textbook controversy (PDF). New Delhi: Delhi Historians' Group.
- Thapar, Romila (9 December 2001). "Propaganda as history won't sell". Hindustan Times.
- "Communalisation of Education: Fighting history's textbook war". Indian Express. 28 January 2002. Retrieved 7 April 2009.
- Thapar, Romila (28 February 2006). "Creationism By Any Other Name ...". Outlook. Retrieved 4 April 2007.
- "Romila Thapar's appointment to Library of Congress opposed"- Rediff article dated 25 April 2003
- Bidwai, Praful (13 May 2003). "McCarthyism's Indian rebirth". Rediff. Retrieved 4 April 2007.
- Gatade, Subhash (June 2003). "Hating Romila Thapar". Himal South Asian. Archived from the original on 9 December 2006. Retrieved 4 April 2007.
- (Text) "Letter of Protest by Scholars and Intellectuals Against the Attack on Romila Thapar". South Asia Citizens Web. 7 May 2003. Retrieved 4 April 2007.
- "And Now in USA ... Attack on Romila Thapar". People's Democracy. 11 May 2003. Retrieved 11 July 2013.
- Nussbaum, Martha Craven (2008). The Clash Within: Democracy, Religious Violence, and India's Future. Harvard University Press. p. 230. ISBN 978-0-674-03059-6.