Somalis have long complained of Amisom's lack of accountability, blaming the mission for numerous deaths in the capital as a result of the shelling of civilian areas. For its part, Amisom has long blamed al-Shabab fighters for this loss of life, accusing them of using civilians as human shields by launching attacks from residential neighbourhoods and marketplaces. However, in November 2010 and January 2011 Amisom arrested three of its own soldiers for shooting civilians in Mogadishu. The three Ugandan soldiers were tried by a military court in the city, but have been sent back to Uganda to serve two-year sentences in a military prison. The force's commander, Major-General Nathan Mugisha of Uganda, has apologised for the civilian deaths and pointed to the convictions as proof that Amisom does not operate with impunity.

The peacekeepers are in a very difficult position, lacking both popular legitimacy and an effective political partner in the TFG. Amisom's refusal to employ Somalis at its base in Mogadishu on security grounds has further alienated locals. The reliance of the peacekeeping force on foreign staff and imported goods minimises the economic benefits of its presence in the country. Amisom's recent attempts to demonstrate accountability could go some way towards changing locals' feelings about the mission, but this stance will need to be maintained and the mission's concern for civilian casualties raised to win and keep popular support.