MSF (Medecins Sans Frontieres) said in a report that the crackdown was denying the injured medical care.
The report also revealed testimony from patients admitted to the main public Salamaniya hospital who said they had been beaten there by security forces.
One of them said he was beaten on a close range rubber bullet wound to his head following surgery.
The agency said it had treated people in their homes after the Gulf kingdom's hospitals and clinics were turned into "places of fear" rather than safe havens for the sick and wounded.
"Health facilities are used as bait to identify and arrest those who seek treatment," said MSF medical coordinator Latifa Ayada as the agency called for the removal of security forces from Salamaniya.
"Wounds, especially those inflicted by distinctive police and military gunfire are used to identify people for arrest, and the denial of medical care is being used by Bahraini authorities to deter people from protesting," she added.
MSF found that Salamaniya hospital was virtually empty during a visit on March 21.
It concluded that the use of the hospital first as a venue for demonstrations and then its occupation by the military, along with the targeting of other health facilities, had undermined the provision of impartial medical care in the country.
However, MSF said that its offer to set up an emergency medical response in Bahrain had fallen through after it failed to secure guarantees from authorities that patients would not be targeted.
MSF underlined that opposition protestors should also guarantee that the hospital would not be used as a rallying point for demonstrations.Continued