The government of Bahrain faces fresh allegations that it systematically tortured people it suspected of taking part in demonstrations against its autocratic rulers earlier this year, and of deliberately undermining the country's health system as 20 doctors go back on trial today for their supposed role in the protests.

One of the world's most respected humanitarian organisations, Médecins Sans Frontières (MSF), alleges that security forces loyal to the tiny Gulf state's authoritarian leader, King Hamad bin Isa al-Khalifa, regularly beat hospital patients who had injuries that could have been sustained during the rallies that started in February.

The MSF testimony is the first to document the existence of what was effectively a torture chamber maintained by Bahraini forces within the hospital. And it provides fresh evidence that retribution was not limited to the alleged ringleaders of the protests.

Jonathan Whittall, MSF's head of mission in Bahrain, has recently returned from the country. He says that troops routinely tortured patients at the main Salmaniya Medical Complex (SMC) in the capital, Manama. "The security forces basically took control of the hospital on 17 March when tanks moved outside and set up checkpoints for anyone entering or leaving. Inside, many of the wounded with injuries that could have been sustained during the protests were taken to the sixth floor, where they were beaten three times a day."

MSF says that young men with injuries such as broken limbs or gunshot wounds were particularly targeted for abuse,

"The hospital became a place to be feared," says Mr Whittall. "One patient was caught trying to leave and he was beaten both at Salmaniya and then later in jail – there was no evidence that he was a ringleader. The situation was so bad some people didn't dare come to the hospital – in some cases, people had no access to healthcare and that is still the situation today."

Some of the injured were removed from hospital, only to reappear later with more serious injuries, Mr Whittall adds. "One guy was brought into the hospital with a sword injury to the head, but he was removed by government forces and disappeared for weeks. His family had no idea what had happened to him until he reappeared with severe brain damage. There were no medical reports or any indication of what had happened to him during his detention."

Unlike protests in other Middle Eastern countries, such as Tunisia or Egypt, where pro-democracy demonstrators have ousted unpopular dictatorships, Bahrain has effectively quelled its protests. Largely, those on the streets, who took over Manama's central Pearl Square, were from the majority Shia population, who argue that they are denied the opportunities afforded to the minority Sunnis. The ruling al-Khalifa family are Sunni.

In March, Bahrain asked neighbouring Saudi Arabia, where the ruling royal family is also Sunni, to send in troops to put down the protests.

The United States last week included Bahrain on its list of human rights abusers, which includes Iran, North Korea, Zimbabwe and Syria. The US had previously been criticised for its lack of action against Bahrain, home to a US naval fleet.

Bahrain's Information Affairs Authority said last week that it intends to sue The Independent for what it described as this newspaper's "skewed perspective and factually incorrect bias that have provided the basis for the daily's assault on Bahrain and its people".

As well as allegations made by a variety of human rights organisations of meting out violent retribution to those it claims took part in the uprising against the state, the Bahraini government has targeted medical professionals, whom it accuses of helping the demonstrators.

The trial of the 20 doctors charged with undermining public order was due to resume today. In other instances, doctors and nurses stand accused of refusing to treat those injured during the protests that had come out in support of the government, and in some cases of killing people.

MSF's Jonathan Whittall: "There is no evidence that doctors turned away any casualties or did anything to destabilise the situation. In fact, the whole thing was so chaotic,” he says.

"There is a lot of anger among the medical community; a massive feeling of injustice. Many of the doctors feel that they have been singled out and targeted because of their standing in society; because they spoke out against the violence, and that some worked at medical stations set up in Pearl Square during the height of the protests." Most of the doctors in Bahrain are Shia Muslims.

The families of several doctors claim that they have been beaten during their detention – claims that have been corroborated by human rights organisations – and that confessions have been extracted under torture. These claims are denied by the Bahraini government.

A series of emails between a surgeon at Salmaniya and the British professor who trained him, published by The Independent in April, gave a vivid glimpse of the pressures on staff.

"I am in the hospital exhausted and overwhelmed by the number of young lethally injured casualties. It's genocide to our people and our hospital doctors and nurses are targeted for helping patients by pro-government militia," he wrote on 15 March.

Two days later Bahraini forces stormed the hospital, saying it had become "overrun by political and sectarian activity". Human rights groups say it was an act of intimidation.

Bahrain's Justice Minister told a press conference in May when the doctors were charged that they had deliberately injured a protester who arrived with a wound on his thigh, causing him to bleed to death. In another case they had operated unnecessarily on a protester who was shot in the head. In both cases the doctors would be charged with "assault that led to death", he said.

According to an Amnesty International report published earlier this month, security officials at Bahrain's Criminal Investigations Directorate forced a number of doctors and nurses to stand for long periods, deprived them of sleep, beat them with rubber hoses and wooden boards containing nails, and made them sign papers while blindfolded.

Bahrain recently lifted its national state of emergency, arguing that the situation has largely returned to normal and that the government is listening to the grievances of demonstrators. This claim is dismissed by several organisations as cosmetic. The lifting of the state of emergency coincided with a decision by Formula One to reinstate the Bahrain Grand Prix, which was postponed in March. Initially the race was rescheduled for October, but was cancelled again two weeks ago when a number of leading drivers expressed concern at returning to the country.

Mr Whittall agrees that the changes have been superficial: "The tanks may have been moved from the front of Salmaniya, but these have been replaced by armoured personnel carriers," he says.