The order was passed by a bench headed by Justice Naresh Patil during the hearing of a public interest litigation filed by advocate Gunratan Sadavarte.
The PIL claims that several people died because there was nobody to attend to them.
The HC asked the government to come out with the terms of reference of the committee within two weeks.
The committee shall record the statements of the relatives besides examining the case papers of the deceased, the HC said.
Meanwhile, Maharashtra Government Medical Officers Association, which had called the strike to press for several demands including implementation of Sixth Pay Commission award, today offered an unconditional apology in the court for causing inconvenience to people.
The court had earlier noted that even newborn children were among those who died during the strike.
Government has maintained that the strike was illegal and participants would lose a part of their salary.
