The international aid agency Doctors Without Borders is to permanently close its operations in Somalia because of repeated “extreme attacks” that it says the country’s authorities are doing little to curb.

The move came as a surprise, and contradicts popular perceptions of growing stability and reconstruction in Somalia that have been carefully crafted by the new government and its international donors.

It also threatens a new period in the troubled nation in which many civilians in rural areas that relied on the famous aid group may be left bereft.

“In choosing to kill, attack, and abduct humanitarian aid workers, armed groups, and the civilian authorities who tolerate their actions, have sealed the fate of countless lives in Somalia,” said Unni Karunakara, the international president of the organization – known by its French acronym MSF, or Médecins Sans Frontières – in a statement.

Many Somalis today have never known their country without war or famine.

The medical organization has operated in the country continuously since 1991 and was one of the few to stay throughout Somalia’s bitter 20-year civil war.

Its 1,500-member staff help hundreds of thousands of people a year, often in areas considered too dangerous for the United Nations or other charities to operate.

But MSF announced Wednesday it could no longer sustain its presence in Somalia because “armed groups and civilian leaders increasingly support, tolerate, or condone violence against humanitarian aid workers,” as the statement put it.

MSF in Somalia last year gave close to 625,000 medical consultations, admitted 41,100 people to hospitals, helped deliver 7,300 babies, immunized 58,000 people, and treated 30,000 malnourished children.

Mr. Karunakara told the Monitor he includes “all civilian authorities” including Somalia’s government in his assessment that leaders are turning a blind eye to attacks on aid agencies.

“We have reached the point where I just don’t see the recognition of the value of impartial humanitarian assistance in Somalia anymore,” he says.

“We’re not therefore able to put our staff in places where they can work. The risks and the compromises that we must make are too high.”

Two international MSF aid workers were shot dead in Mogadishu in December 2011, adding to 14 other staff who have been killed in the country since 1991, a rate of one every 17 months.

Two Spanish MSF medical logistics workers who had been held hostage in Somalia for close to two years were released last month.

“I want to reiterate that the kidnapping was simply the latest in a series of incidents since we have been present in Somalia, but yes, it was the last straw,” Karunakara says.

Blaming the shutdown on armed groups that threaten MSF staff, supplies, and local partner organizations was no surprise, says Andy Atta-Asamoah, Horn of Africa analyst at the Institute for Security Studies in South Africa.

But also pointing the finger at "civilian authorities" was a powerful addition to the MSF statement, he says.

“No matter which way you look at it, this will be a huge blow. These aid agencies, unlike the United Nations, are not aligned to the government, so they can help people in places where others can’t,” Mr. Atta-Asamoah says.

'“Those people, most likely, will now not be reached. That’s the humanitarian implication."

Atta-Asamoah also speaks of larger implications: “The talk of authorities tolerating armed groups seems to me to match the perception growing in Mogadishu that certain political leaders have lost their appetite for the fight against Al Shabab," speaking of the Islamic radical group that has risen in recent years in the Horn of Africa.

“The momentum that was there has really slowed down.”

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Karunakara steered clear of explicit political statements, but added that MSF is the only medical organization working in many areas. It is feared that other aid agencies and local health authorities will be unable to take up the slack.

“Ultimately, civilians in Somalia will pay the highest cost,” Karunakara says.