Protesters wounded in anti-government rallies in Syria have been tortured and abused inside hospitals, and in some cases deliberately refused medical treatment, according to a damning report by Amnesty International.

The human rights group said there was compelling evidence that the Syrian government was using hospitals as "instruments of repression" in its ongoing efforts to crush opposition. The report said medical staff, nurses and security officials had all physically and verbally attacked patients. Seriously wounded demonstrators suspected of taking part in anti-government rallies had been carted off from hospital to military jails, Amnesty added.

The report paints a picture of human rights violations in four government-run hospitals, in the cities of Banias, Homs and Tell Kalakh, with the military trawling wards in search of the opposition. The situation has grown so bad that wounded protesters are now seeking treatment in makeshift field hospitals instead, it says.

Security officials have also accused doctors of siding with demonstrators – arresting them and taking them away. Other Arab states seeking to crush their own uprisings have used similar methods of intimidation. Last month 20 medics in Bahrain were jailed for five to 15 years for treating activists wounded in anti-government protests, prompting international outrage.

"It is deeply alarming that the Syrian authorities seem to have given security forces a free rein in hospitals and that in many cases hospital staff appear to have taken part in torture and ill treatment of the very people they are supposed to care for," Amnesty's Middle East researcher Cilina Nasser said on Tuesday.

"Given the scale and seriousness of the injuries being sustained by people across the country, it is disturbing to find that many consider it safer to risk not having major wounds treated rather than going to proper medical facilities," Nasser added.

The UN estimates more than 3,000 Syrians have been shot dead during the violent government crackdown on protesters. Thousands have been injured. The uprising began at the start of the year but escalated from mid-March, with protests in numerous Syrian towns as well as the capital, Damascus. On Monday, the US withdrew its ambassador to Syria over safety fears.

The report cites several examples of treatment being denied, in contravention of medical ethics. In one case a patient, 28, who was shot in the foot on 16 May, was told by a doctor at Homs military hospital: "I'm not going to clean your wound … I'm waiting for your foot to rot so that we can cut it off."

One severely wounded patient, Ahmed, woke from surgery to discover seven or eight security officials standing round his bed. One witness said: "He opened his eyes and said: 'Where am I?' They all suddenly jumped on him and started beating and hitting him … They shouted foul language at him and said: 'You pig, you want freedom, eh?'" Ahmed was later taken from hospital. His whereabouts are unknown.

In another case, soldiers took an injured 21-year-old protester to the Homs military hospital morgue and asked him to identify bodies of men from his hometown. He recognised three – but failed to identify the others. Officials locked him in, leaving him shivering among the bodies. "After around one or two hours, I felt so cold deep in my bones and couldn't stop shivering," he recalled, adding that he made up some names in order to "save myself".

But some medical staff have behaved with exemplary professionalism. In March and April the director of Homs hospital called four meetings, instructing his staff to treat all patients – military and civilian – without discrimination. Others who have taken a principled stand have been summoned for interrogation by Syria's feared internal security bureau. Some have fled the country.

James Walsh, an Amnesty researcher on health and detention, said the level of abuse in Syrian hospitals was "quite striking". But he pointed out that there were also medical professionals who were taking significant risks to protect patients. "It's a complex mix of failed ethics, where people are in a coercive environment and where being a hero is not necessarily going to be an easy thing." He conceded that given the secrecy involved it was difficult to gain a clear picture from outside.

Amnesty International also found that patients had been removed from hospitals. On 7 September, security forces looking for an alleged armed field commander opposed to the government raided al-Birr wa al-Khadamat hospital in Homs. When they did not find him, they arrested 18 wounded people. A staff member present during the raid recalled seeing at least one unconscious patient having his ventilator removed before he was taken away.

Cilina Nasser added: "Syrian medical workers are being placed in an impossible situation – forced to choose between treating wounded people and preserving their own safety. The Syrian authorities must see sense and urgently act to ensure that all patients are treated equally, without discrimination based on their suspected political loyalties or activities."