The former Tamil Nadu chief minister, however, absolved Modi of any personal culpability in the episode.
Without naming Irani, he said that "unilateral" and "authoritarian" interference by Modi's ministers on such issues will impact both the youth of the country and the nation's peace.
"Though it seems that Prime Minister Modi doesn't place importance on needless issues like banning a democratic group, his ministers interfering unilaterally and in an authoritarian manner in such issues will impede youth's thought process and affect the nation's peace," he said.
"Because of this incident, the otherwise peacefully functioning institute has turned into a war zone," he said.
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Karunanidhi also asked if the AIADMK government, "by not making any explicit statement against the ban and remaining silent," was supporting the Centre on this issue.
IIT-M is in the eye of a row over derecognition on Friday of the students group, many of whose members are Dalits, following a complaint that it was critical of Prime Minister Modi.