U.N. Deputy Secretary-General Jan Eliasson gave the death toll at a news conference Thursday at U.N. headquarters.
Eliasson said Uganda and Burundi, which supplied most of the troops for the AU force, “have paid a tremendous price.”
A spokesman for the force, Ali Aden Hamoud, says he cannot confirm or deny the death toll.
“That responsibility belongs to each one of those contingents, or troop-contributing countries,” he said.
Eliasson said the al-Shabab threat has receded but still exists and that the AU force, known as AMISOM, still “plays an absolutely crucial role” in Somalia.
AU soldiers arrived in Somalia in 2007 and were involved in heavy fighting with al-Shabab in Mogadishu for several years.
The capital is largely calm these days, although al-Shabab still carries out periodic attacks like a suicide bombing last Sunday that killed eight people.
The East African nation is attempting to emerge from more than 20 years of chaos and war under a new government formed last year. Donor nations pledged $300 million for security in Somalia at a conference in London this week.