Justice Girish Gupta annulled the order by MCI and the state's Health University issued last year terming it as "illogical".
The court observed that the alleged use of infrastructure of Haldia Institute of Dental Sciences and Research by the medical college could not be a ground for cancellation of license.
The court noted that while the law says that there should be proper infrastructure to run a medical college, it does not say that a medical college and a dental college cannot share the same infrastructure.
Both these institutes were managed by Laxman Seth's Indian Centre for Advancement of Research and Education and are based in Haldia, a town about 160 km from here.
Seth, chairman of ICare, was recently granted bail by the high court in connection with a case of disappearance of several Nandigram agitators in 2007.
Haldia strongman Seth had been arrested from Mumbai by the CID and was lodged in jail for 114 days before being granted bail.