A four-member bench of the Appellate Division led by Justice Surendra Kumar Sinha gave the order on Sunday asking the college authorities to pay the fine within ten days.
In case of default, the colleges will have no enrollment right for the 2016-17 session.
The medical colleges are MH Samorita Medical College, City Medical College, Nightingale Medical College, ZH Sikder Medical College, AR Medical College, East West Medical College, Tairunnessa Memorial
Medical College, Aichi Medical College, Care Medical College and Ashiyan Medical College.
In the order, the court says that the DU authorities will get a half of the amount while National Liver Foundation and kidney foundations will get the other half.
The DU will have to open a FDR with the money and its interest will be spent to give stipend to its poor students. The NBR tax will not be applicable for the interest.
The Health Ministry along with the DU will oversee the order's implementation.
The ten colleges are run by the DU which along with the government had set that the MBBS and BDS degree aspirants must have 120 marks of 200 to be eligible for the enrolment. But the authorities allowed the
admission to a total of 153 students violating the benchmark.
However, the DU authorities had traced the violation and decided to not let the 153 students to appear in the first professional exam.
On June 13 last year, the students moved with a writ petition against the DU decision and the High Court ordered to provide registration and admit cards to the students.
Later, the DU moved with the Appellate Division against the High Court order and the latest decision came after the hearing.