Doctors in 14 medical colleges participated in the one-day "mass bunk" stir, including around 1,500 from Mumbai colleges like KEM, Sion, Nair and JJ hospitals.
The doctors have warned that if their demands are not met by Friday, they would go on an indefinite mass bunk stir from January 31.
OPD admissions as well as planned surgeries, both of which are looked after by the residents, have been affected, said Sunny Khandare, president of Maharashtra Association of Resident Doctors (MARD).
"However, it is the government who is to blame for this situation. They forced us to take this step," he told PTI.
As per a state government policy, stipend of resident doctors in medical colleges must be reviewed every three years, he said.
After the review in 2009, the doctors were to receive an increased amount last July. However, they did not get the entitled raise of around Rs 13,000, he said.
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"We are receiving a monthly stipend of Rs 31,600 instead of the Rs 44,000 we were supposed to get since July," he said.
The doctors have also demanded that the existing bond policy, requiring resident doctors to serve in rural hospitals for a year after graduation, must be implemented properly.