Bahrain's already tarnished reputation for human rights will receive a body blow today with the cancellation of a major conference on medical ethics in the tiny island monarchy, and the resignation of the Irish director of Bahrain's principal medical school.

At least 20 civilians were killed by government forces – opposition leaders say the figures is four times as great – in the failed uprising by the majority Shia Muslim community against the minority Sunni-led government of King Hamad bin Isa al-Khalifa two years ago. Security forces stormed hospitals in the kingdom and tortured patients in medical care, tearing apart the hitherto non-sectarian health service. The Royal College of Surgeons in Ireland (RCSI) – which trained many of the doctors later arrested by the regime – was bitterly criticised after the violence for not condemning government brutality.

But Médecins Sans Frontières (MSF) will today announce its decision to cancel next month's international meeting – in which medical and human rights experts were to speak for two days on "medical ethics and dilemmas in situations of political discord or violence" – while Professor Tom Collins, president of the Medical University of Bahrain, will tell his 1,100 students and 240 staff at lunchtime that he is resigning in protest at the cancellation. The university is run by the RCSI and was co-sponsor of the conference with MSF.

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At least 40 Bahraini doctors, many of them attached to the RCSI medical university on the island, were arrested and charged after the mini-uprising of 2011 – four are still in prison – although Professor Collins has pleaded for their release. A prestigious roster of speakers was to have included Professor Patrick Roe, the president of RCSI, a consultant general surgeon at Beaumont Hospital in Dublin, Anastasia Crickley of the United Nations Committee on the Elimination of Racial Discrimination, and Baroness Nuala O'Loan, Northern Ireland's first – and highly controversial – police ombudsman from 2000 to 2007. Many attribute Catholic trust in the new Police Service of Northern Ireland to the work of Lady O'Loan. The organisers were to show a film, Access to the Danger Zone, on MSF doctors in Afghanistan and other wars, narrated by Daniel Day-Lewis.

For months, both the MSF and RCSI tried to persuade the Bahraini royal family to allow the conference. They say they were forced to cancel it when they failed to receive written permission from the authorities to hold the meeting at the Intercontinental Hotel in the capital, Manama. In an exclusive interview, Professor Collins – whose resignation will take effect in June, just over half way through his tenureship of the medical university – said that he had met the Bahraini Crown Prince, Salman bin Hamad bin Isa al-Khalifa, in the company of an MSF official. "He gave his verbal approval to myself and MSF," Professor Collins said. "This was in the late autumn of last year. He said: 'I want this conference to happen'. But the written permission never arrived."

According to his colleagues, Professor Collins felt there were important parallels between the situation in Bahrain and that in Northern Ireland, which made the conference all the more valuable for Bahrain. "There was a sectarian dimension to the uprising in Bahrain – but in neither Bahrain nor Northern Ireland was it as initially sectarian as it was made out to be," one of the professor's fellow teachers said. "In both cases, the authorities responded to a political problem with a security response – and drove the sectarian wedge deeper. Then came internment in Northern Ireland and Bloody Sunday, all of them disproportionate responses, radicalising the minority [Catholic] population. There has now been a high level of radicalisation among the Shia in Bahrain. The lesson from Northern Ireland is that you can create political engagement providing you have institutional and legitimate frameworks to guarantee human rights."

This view alone may have made the conference highly charged in the eyes of the Bahraini royal family, which called its own public inquiry into the violence in 2011, in which police fired live rounds at unarmed Shia protestors who – after the Arab uprisings in Tunisia and Egypt – believed their time had also come. But they protested too soon. With no post-revolutionary programme, the thousands of demonstrators were driven from their centre at Pearl Square; many were arrested in hospitals after being wounded by police officers. The Pearl monument was subsequently demolished by the government. The Bassiouni commission of inquiry, called by the royal family, delivered a harsh report on repression and torture by the authorities, but was never acted on. Professor Collins wrote to Professor Cherif Bassiouni with his own recommendation to free still-imprisoned doctors. He received no reply.

Bahrain's royal family – dominated by Saudi Arabia, whose soldiers were sent into the island as part of a Gulf Co-operation Council force to crush the uprising – now faces a hard task to explain why an international conference on medical ethics cannot be held in the kingdom. Dr Bart Janssens, MSF's director of operations, says that "after a year of discussions, we still do not have the support we need to go ahead with the conference. As a result, we are forced to conclude that today in Bahrain, it is not possible for medical professionals and international impartial participants to have a conversation about medical ethics." According to Dr Janssens, who is from Belgium, MSF will look for other locations in the Gulf.

Professor Collins, who has been deeply upset by the violence, says that he does not wish to harm the RCSI, whose university in Bahrain makes a profit of around $2m (£1.3m) a year – although it is currently $50m in debt – and that he wants to contribute to stability in Bahrain. British trade and the presence of the US Fifth Fleet in Bahrain have effectively silenced any serious criticism from Messrs Cameron and Obama. King Hamad was invited to the Queen's Golden Jubilee.

MSF has repeatedly proposed to the Bahraini ministry of health that it would accompany patients to health centres to verify that staff, patients and security personnel were acting in compliance with medical ethics. The ministry failed to reply. Jonathan Whittall, of MSF in the Middle East, says that health facilities in Bahrain became a battleground.

"At the beginning of the uprising, the opposition used the Salmaniya Hospital as a launch pad for protests – after which the government disproportionately reacted by militarising health care," he says. "Hospitals became places to be feared. Our conference was designed to raise the problems of medical ethics and to restore trust in the health system in Bahrain. It's not only in Bahrain but in the region that discussions of this kind would have a benefit for patients to approach hospitals without fear. Failing to have this conference is not only a setback on this problem for Bahrain, but for the region as a whole."

Bahrain's royal family is divided over how to respond to the majority Shia demand for more political power. Crown Prince Salman is a reformist – hence, presumably, his desire to hold the international conference on medical ethics – but others, under the influence of the Saudis, believe that no way should be opened to reform.

During the 2011 demonstrations, some Shia Bahrainis asked the Crown Prince to join them at Pearl Square. One Shia woman even said that the protesters would carry Prince Salman on their shoulders around the square to show their support for him. But he did not come. And no protester would make such an offer today.