Medical aid agency Doctors Without Borders confirmed Friday that two staff members, a Belgian and an Indonesian, were killed by a gunman in the war-torn Somali capital Mogadishu.

"It is with great sadness that Medecins Sans Frontieres (MSF - Doctors Without Borders) confirms that two MSF staff members were killed yesterday... as a result of a shooting in the organisation's compound," a statement said.

Philippe Havet, a 53-year-old emergency coordinator from Belgium, and Andrias Karel Keiluhu, known as Kace, a 44-year old doctor from Indonesia, were helping provide emergency medical assistance in famine-hit Mogadishu.

Havet was killed during the shooting, but Keiluhu died after surgery in hospital in Mogadishu, the organisation added.

"While one of the aid workers died during the shooting, the other was transferred to a hospital and died after surgery in the evening," MSF said.

"We are deeply shocked by this tragic event and we will greatly miss Philippe and Kace."

The bodies were flown out of the Horn of Africa nation Friday, along with other international staff, said Mohamed Ibrahim, a Somali security official.

"The dead bodies of the two MSF workers have been taken to Nairobi, they were picked from Medina hospital where one of them died on Thursday night," he said.

The shooting was the latest attack on humanitarian officials in Somalia, one of the most dangerous places in the world for aid workers, but MSF said it remained committed to help the people of Somalia.

"MSF will be relocating some staff for security reasons, but remains committed to continuing our humanitarian work in Mogadishu and elsewhere in Somalia," the statement added.

Security forces arrested the gunman, who witnesses and police identified as a Somali employee with MSF.

"The exact circumstances of the shooting are not yet clear," MSF added. "Our priority is to take care of those most affected by this tragedy, in particular the families and the colleagues of the victims."