The timing of the notice, served on September 20, and the fact that "less than 1 per cent of IT returns are scrutinised", suggest that the move may be an act of "state vengeance and intimidation," Mr Mander, who is on a nation-wide campaign against mob lynchings, claimed.
A senior Income Tax official, speaking on condition of anonymity, however, said such notices are "routine" and "nothing more should be read into it".
Hindu right activists, including cow vigilantes, have been blamed for several incidents of lynching in recent times, in states like Uttar Pradesh, Rajasthan and Jharkhand.
The institute, founded in August 2000 by Professor Ghanshyam Shah, Professor S Parasuraman, Professor Jean Dreaze, NC Saxena and Mr Mander, received by email a notice under Section 143 (2) of the Income Tax Act for scrutiny of its IT returns for the assessment year 2016-17, Mr Mander said in a statement.
Mr Mander is currently visiting various states where lynchings have taken place in the recent months as part of the initiative- 'karwan-e-mohabbat' (KeM) or the caravan of love- which he has described as a journey of love, atonement and solidarity.
"We are happy to subject ourselves to any scrutiny, and will fully cooperate with the investigation, as we believe in public accountability.
"But I would like to state categorically that no amount of state intimidation of the organisations that I am associated with, would succeed in silencing my public dissent with policies and ideologies that I believe are detrimental to India's constitutional values," he said.
The scrutiny of income tax returns filed by the organisation is being conducted by the exemptions wing of the department that looks after the work of charitable and social organisations, and the notice mentions that all communication in this context will be conducted electronically.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.