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Abducted, drugged and gang raped in Somalia: a young mother details the most brutal of allegations against African Union troops and Somali soldiers in a case causing widespread anger.

"The soldiers raped me... I tried to defend myself but they beat me badly and I passed out," she said, speaking to the Somali Channel television about the attack earlier this month.

She alleged she was stopped on the streets of Mogadishu by three soldiers from the national army, blindfolded and forced into a car, before being handed over to African Union troops, where she says she was repeatedly raped.

She has needle marks on her arms from where she says drugs were injected during the several hours long assault in the Maslah compound, a Ugandan troop base on the outskirts of Mogadishu.

"There were other women in the room... one of the them badly bleeding," she added, speaking from a hospital bed.

The woman, in her late 20s with a young baby, was unconscious during the attack and says she does not know how many men raped her. She was later thrown back onto the streets.

AMISOM, the 17,700-strong United Nations-mandated force that supports the government in its fight against Al-Qaeda-linked Shebab insurgents, said it has launched an investigation together with the Somali army.

"Appropriate action will be taken once the facts of the case have been established," AMISOM said in a statement.

Somalia's Prime Minister Abdi Farah Shirdon said in a statement that the government was "deeply troubled by the alleged rape... involving a number of personnel from AMISOM."

AMISOM, fighting since 2007 in Somalia and funded by the UN and European Union, insists it "strongly condemns ... sexual abuse or exploitation."

The force is mainly made up of troops from Uganda, Burundi and Kenya, with smaller numbers from Djibouti and Sierra Leone.

The case threatens to badly dent the reputation of the force, and play into the hands of the Shebab.

Shebab fighters are themselves accused of horrific attacks and rape, but the extremists' spokesman Ali Mohamed Rage gloated at the rape reports.

"Somali soldiers first abduct the girls and rape them, they also share them with AMISOM troops," Rage said.

"The Somali troops are the remnants of the former warlords, they are killing their people and raping our daughters and mothers... the African Union troops are brutal."

The allegations come at the same time as the country reels from a surprise pullout by medical aid agency Doctors Without Borders (MSF), ending work in Somalia after more than two decades following a "barrage of attacks."

On Tuesday, MSF president Unni Karunakara said the "painful decision" of pulling out "came at a moment when world leaders, for the first time in decades, began making positive noises about a country on the road to recovery and with a stable government."

Rape is pervasive in Mogadishu, but the extreme nature of the woman's allegations and the accusations of AMISOM involvement have shocked many.

In the first six months of 2012, some 800 cases of sexual violence were reported in Mogadishu alone, according to the United Nations Office for the Coordination of Humanitarian Affairs (OCHA), which refers to the rapists as "unknown armed men and men wearing military uniform."

Many more cases are believed to have gone unreported.

"Sexual violence in Somalia is one of the most serious and urgent human rights challenges facing the government and people of Somalia," said Nicholas Kay, UN special representative for the country.

Kay, who expressed his "grave concern" at the rape allegations, has demanded investigations be "rigorous and prompt."

"If there is a case to answer, any perpetrator should be prosecuted," Kay said in a statement.

But Maryan Qasim, Somalia's minister for human development, insisted there was "major exaggeration and inflation of the number of attacks."

In an interview with Somali media, she claimed women were taking money to allege that they had been raped, and that it is "better for a girl to be shot instead of being photographed and publicised" while making such allegations.

Somalia's army, an often rag-tag force incorporating militia fighters, has repeatedly been accused by rights groups of a string of abuses against women, including rape.

Even reporting on rape in Mogadishu carries its own risks: a Somali journalist and a rape victim he interviewed were both sentenced to a year in prison in February, but they were released after two months in jail after the case sparked widespread international criticism.