Mukherjee was conferred with the D Litt degree during the 29th annual convocation of the university at Dr Shyama Prasad Mukherjee Stadium near here.
Goa Governor Mridula Sinha, who is also the university's chancellor, awarded the degree to Mukherjee.
Goa Chief Minister Manohar Parrikar too was present on the occasion.
A minute's silence was observed during the convocation to pay homage to the CRPF personnel who were martyred in Chhatisgarh yesterday in a Naxal attack.
Earlier, various degrees and diplomas were awarded to the univerity students.