A division bench of Chief Justice Mohit Shah and Justice M S Sanklecha directed the Samiti to complete its inquiry into the alleged fraud within two months.
The direction was passed in a public interest litigation filed by social activist Balasaheb Jambhulkar alleging that the institute showed inflated expenditure on students in order to the Samiti to approve higher fees.
Jambhulkar's counsel Anil Anturkar had argued that the institute had defrauded students and government into paying excess fees to the tune of Rs eight crore in just two years since 2010.
MET's co-founder Sunil Karve was, however, supporting the petition and had alleged that Bhujbal and his family had misappropriated funds of the institute.
Karve had in December 2013 written a letter to the police alleging that there is misuse of trust funds.
In his complaint, Karve alleged that the institutes at the Nashik campus have been showing inflated expenditures on technology development fund and student activity funds since academic year 2009-10 to the tune of Rs 7.88 crore.