"There is no interference. We are getting what we want," Chakrabarti told reporters here when asked about the MHRD interference.
When asked about budget cuts, he said they have discussed it with the Ministry and were hopeful of getting more grants.
Earlier in May, IIT-Madras had derecognised a students' group following a complaint that it was critical of Prime Minister Narendra Modi.
The incident had triggered protests from political parties who claimed it was due to the MHRD interference.