As the strike entered the third day, the HC asked the state government to refer critically ill children of Niloufer Hospital to private hospitals.
As many as nine children have died in Niloufer since the doctors went on a lightning strike on Sunday night.
The junior doctors had struck work protesting against the alleged attack on their colleagues by MIM MLA, Mr Afsar Khan, and a patient's attendants.
Medical services in other government-run hospitals too were hit as junior doctors went on strike.
The HC, which was hearing a petition on the issue by an advocate, Mr Raju, said that junior doctors were disrupting the functioning of the hospital just as the MLA had done.
A division bench comprising acting chief justice Bilal Nazki and justice Ramesh Ranganathan directed the state government to inform the court about the alternative arrangements made to treat patients. It also directed that the striking doctors be not allowed to enter the hospital.
Justice Nazki said, "They (junior doctors) are doing the same thing what the MLA had.