The decision to cancel their registration was taken by DMER after it found that these doctors have refused to work in rural areas for a year - a mandatory provision made by the state government.
According to DMER, these doctors have even failed to pay the penalty incurred for not serving in rural areas.
In all, 4,548 doctors have faced action. They graduated from government-run medical colleges in the state between 2005 and 2012 and have neither served in rural areas nor paid the fine, it said.
A DMER official said, "If the doctors do not serve the bond, they must pay a penalty, which is Rs 10 lakh for an MBBS, Rs 50 lakh for post-graduates and Rs 2 crore for superspeciality doctors."
Head of DMER Dr Pravin Shingare said all the doctors who have faced action, had been given sufficient time to honour their commitment to serve in rural areas or pay the penalty.
"We took this firm step as these doctors violated both the clauses," he said.
A senior official of the state medical education department, said every medical practitioner needs to renew his or her registration with the Maharashtra Medical Council.
"The objective of the bond is to give doctors exposure to complicated cases. It is a highly educative and learning experience for newly-graduated doctors. Hence, we want them to go to rural areas and work for at least a year," the official said.
The government also provides reasonable allowances for doctors serving in tribal areas. The wages are also high, he said.
Dr Sagar Mundada, the chairman of the youth wing of Indian Medical Association (IMA), said, "Nobody is complaining about remuneration, but the real issue is poor infrastructure at primary health centres, where these doctors serve as a part of their bond."
"Except for a handful of medicines, no other drugs are supplied. Other essential materials provided are of low quality and in poor quantity. The quarters provided to these doctors are poorly maintained and still they are expected to stay there for a year," he said.
"The government forgets its responsibility of maintaining infrastructure and keeping a smooth supply of medicines and other necessary materials. Minor surgery has to carried out at PHCs and not a single equipment is available at the centres.
In such cases, a doctor faces the wrath of people," Dr Mundada said.