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National workers with MSF conduct a screening and measles vaccination clinic inside a section of the large Tarabunka camp for displaced persons in Mogadishu, Somalia on Sept. 8, 2011.Peter Power/The Globe and Mail

For more than two decades, despite war and chaos and the murder of 16 of its aid workers, Doctors Without Borders has maintained its crucial medical aid to Somalia. But now a new wave of extreme attacks has pushed it into an unprecedented response: closing down all of its clinics and hospitals in the impoverished country.

The agency, also known as Médecins Sans Frontières (MSF), said the "last straw" came when it discovered that some of Somalia's official authorities were supporting or condoning the lethal attacks on its aid workers.

In one shocking case, the convicted killer of two MSF aid workers was mysteriously freed from prison and vanished into the streets after serving only three months of a 30-year sentence, it said.

It is the first time in 22 years that the agency has shut down all of its medical work in Somalia, and a stark reminder of how dangerously violent and terror-prone the country remains, despite recent optimism that the country was stabilizing. The sudden withdrawal of the famed relief agency will leave hundreds of thousands of Somalis without humanitarian aid. Most have no other source of medical care.

"It's a massive and unprecedented decision, and incredibly painful," said Arjan Hehenkamp, a senior director of MSF's global operations, in a conference call with journalists on Wednesday.

Within minutes of the announcement, an MSF hospital in southern Somalia was already attacked and looted by militants from al-Shabaab, an armed militia with links to al-Qaeda.

Optimistic reports this year, including on CNN, have claimed that Mogadishu is enjoying an "economic renaissance" and attracting foreign tourists with its new-found stability. Oil companies, including at least one Canadian company, were negotiating deals for Somalia's oil resources.

But those reports soon seemed very premature. In June, militants attacked a United Nations compound in Mogadishu, killing 22 people. A car bombing killed three people at the Turkish embassy in Mogadishu last month, and several government officials have been assassinated in recent weeks.

MSF is famous for enduring severe risks in the world's toughest and most dangerous war zones, long after other relief agencies have given up. But it announced on Wednesday that it is shutting down its activities in Somalia after a "series of extreme abuses" – including the killing of two staff in Mogadishu and the kidnapping of two Spanish MSF aid workers who were abducted in a refugee camp and held hostage for 21 months in southern Somalia.

With about 1,500 staff in Somalia, the agency is one of the biggest providers of medical care in the war-torn African nation. It helped more than 620,000 patients last year alone in a dozen towns and cities across Somalia, and it has given care to a further 300,000 Somalis so far this year.

The closure is "one of the hardest decisions MSF has had to make in its history," the agency said in a statement. It is the first time in 22 years that the agency has shut down its medical work in Somalia. But it had already been forced to use armed guards to protect its staff in Somalia – a precaution that it does not take in any other country.

The decision to withdraw from Somalia was not only because of the extreme violence, but also because the attacks were increasingly supported or tolerated by civilian authorities, MSF said.

Civilian leaders in Somalia are playing a role in "the killing, assaulting and abducting of humanitarian aid workers … either through direct involvement or tacit approval," it said in the statement.

In some cases, it said, the attacks have been supported or condoned by the same armed groups or civilian leaders with which MSF has to negotiate promises of security for its humanitarian work.

"Ultimately, civilians in Somalia will pay the highest cost," said Unni Karunakara, the international president of MSF, in a statement on Wednesday.

"The armed groups' targeting of humanitarian aid and civilian leaders' tolerance of these abuses has effectively taken away what little access to medical care is available to the Somali people."

He said the "risks and compromises" for the MSF staff have become too high for the agency to accept.

"In choosing to kill, attack and abduct humanitarian aid workers, these armed groups and the civilian authorities who tolerate their actions have sealed the fate of countless lives in Somalia."

In a conference call with journalists later, Dr. Karunakara said the withdrawal will leave "huge gaps" in health care.

But some of Somalia's leaders were "turning a blind eye" to the attacks on MSF aid workers, and they weren't respecting MSF's independence and impartiality, he said.

"We have now reached our limit," he said. "We cannot work in such a volatile environment."