The HC bench of Justice FRM Nazmul Ahasan and Justice KM Kamrul Kader passed the order following a writ petition.
The commission will have to be formed comprising experienced physicians and skilled persons.
In its observation, the court said business cannot be done with the life of people in terms of treatment.
Although the government keeps aside huge allocation for the health sector, medicines are not found at hospitals and those are available in markets, it said.
Referring to Anti-Corruption Commission’s recent drives to 11 government hospitals where it found 40 percent physicians absent in the capital while 62 percent at district level, the court said it reveals the actual scenario of the health sector.
The HC also issued a rule asking the government to explain as to why the section 4 of the Medical Practice and Private Clinics Laboratories (Regulation) Ordinance-1982 should not be declared illegal.
Health Secretary, Director General of the Directorate General of Health Services (DGHS) and presidents of President of Bangladesh Medical and Dental Council have been made respondents to the rule.
On February 4, Advocate Abdus Sattar Palwan filed the writ with the High Court seeking its directive to stop private practice by the physicians of government hospitals during their office hours.
The writ was filed after a report titled ‘Physician at his chamber, patient dies at hospital’ was published in national dailies and online portals on January 29.
Babul Hossain, 40, who was suffering from cardiac problem, died at Laxmipur Sadar Hospital due to negligence of doctors as duty doctor Bhabani Prasad Roy was absent at that time. Bhabani Prasad was at his chamber in Dakkhin Temuhani of the district during the incident.