The rule was introduced by the Centre in June and the Maharashtra government started implementing it from July 1.
"We fail to understand the rationale behind the rule," a division bench of Chief Justice Mohit Shah and Justice N M Jamdar said while staying the rule.
The bench was hearing a petition filed by city radiologist Rajeev Zavkar stating that in 2002 he opened his own clinic in suburban Mahim and at the same time had also been practising in three other centres.
According to Zavkar, the amendment to the act curbs his right to practise his profession. He argued that it would not be correct for a doctor to be present in a hospital and in case of emergency not able to attend to the patient because he is already registered at two clinics.
Government pleader G W Mattos opposed the petition stating that the amendment was introduced with a view to keep a check on the malpractices carried out by radiologists.
Granting an interim stay on the rule, the court directed both state and Centre to file their replies on August 27.