An AU-led team headed to Somalia on Monday on a delayed mission to assess security before the deployment of peacekeepers to the country which collapsed into anarchy in 1991 and has since been run by rival clan-based warlords.
The future AU peacekeeping mission is to help Somalia's fledgling government re-establish itself at home. The government tentatively plans to return on 21 Febuary.
Muslim groups rally
Monday's protests, led by a federation of Islamic groups, were particularly aimed at plans to send troops from Ethiopia, a traditional rival of Somalia in the Horn of Africa, witnesses said.
The protests echoed those held on Friday, where the federation called for "holy war" if non-Muslim troops came to Somalia.
A senior African Union official said the fact-finding team included officials from the AU, Arab League and the Inter-Governmental Authority on Development (IGAD), an East African peace resolution body.
"They left for Somalia today," the senior AU official told Reuters. "They have left for Mogadishu."
The trip had been due to begin on Friday but was delayed over security concerns, after BBC producer Kate Peyton was shot dead on Wednesday in one of the capital's less risky neighbourhoods.
Somali President Ahmad wants
an African-Arab force
Kenya, Uganda, Djibouti, Ethiopia and Sudan - all members of IGAD- are initially due to provide troops and equipment pending the deployment of a African Union peace support mission, according to AU officials.
Somali President Abd Allah Yusuf Ahmad has said he wants a combined AU-Arab League force of 7500 troops to facilitate the government's return.
Some prominent warlords in his administration have argued militias are all the military muscle required.
Somalia's government was formed at peace talks in the safety of Kenya last year to end the lawless rule of militias which banded together to depose military dictator Mohamed Siad Barre in 1991.
Somalis traditionally resist outside interference and the last peacekeeping mission there ended in a bloody and humiliating withdrawal by US and United Nations troops in the mid 1990s.