"In Tamil Nadu they should sing the Tamil anthem or invocation," he said, adding "It (religious song being recited) is condemnable".
At government functions in the state, only "Tamil Thaai Vazhthu" (invocation song of mother Tamil), penned by Manomaniam Sundaram Pillai, is played in the beginning and the national anthem towards the end of the events.
On Monday, however, students sung 'Maha Ganapathim Manasa Smarami', penned by late poet Muthuswami Dikshithar as the invocation song soon after arrival of dignitaries for the foundation stone laying ceremony of National Technology Centre for Ports, Waterways and Coasts, to be set up along with IIT Madras.
Professor Bhaskar Ramamurthi, Director of IIT Madras, said "It was not a planned recital. Students had decided on the Sanskrit song. Tamil invocation would be played in future."
Senior Minister D Jayakumar on Tuesday called the explanation unacceptable. He said "Amma government will never accept anything that is tantamount to throwing away such traditions."
A few student groups had staged a protest outside IIT Madras on Tuesday accusing the institute of imposing Hindu and Sankrit songs at a government-run institute of higher learning.
In a statement, DMK Working President MK Stalin slammed the BJP. He said "It appears to be a planned attempt to mock Tamil culture and traditions by ignoring the Tamil anthem. In a secular institution of higher learning they've recited in praise of religion."
Only recently the Junior Pontiff of the Kanchi Mutt in Tamil Nadu had come under criticism for not standing for the Tamil anthem during a book launch. The mutt had said the pontiff was meditating at that time and that religious heads do not subject themselves to these traditions.
IIT Madras has been ranked number two in the all India rankings by the National Institutional of Ranking Framework.