K. N. Panikkar has written and edited a number of books, including A Concerned Indian’s Guide to Communalism and the ICHR volume on Towards Freedom, 1940: A Documentary History of the Freedom Struggle (suppressed and withdrawn from press by the former Bharatiya Janata Party-led regime, now forthcoming).
His methods and his expressed positions in public life have evoked harsh criticism from exponents of Hindu nationalism, particularly during the period of Bharatiya Janata Party government of 1998 to 2004.
Panikkar has been active in criticising the rise of "Nationalist" history in India. His books include Against Lord and State: Religion and Peasant Uprisings in Malabar; Culture and Consciousness in Modern India; Culture, Ideology and Hegemony – Intellectuals and Social Consciousness in Colonial India, and Before the Night Falls.
He was appointed by the government of Kerala as chairman of an Expert Committee that looked into the complaints raised from various quarters concerning new textbooks introduced to state-supported schools. The committee submitted its report in October 2008.