The suspension on Thursday comes in the wake of a damning report by Human Rights Watch which has accused troops with the internationally-funded African Union force in Somalia, AMISOM, of preying on vulnerable women and girls.
"We are doing a general appraisal on performance of the force," Uganda's defence and army spokesman Paddy Ankunda told the AFP news agency.
"It's not sexual harassment alone," he said, but added the concerns were "one aspect we are looking at."
"Those are allegations. We are investigating. Until the investigations are completed that's when we will know their involvement [in sexual abuse], but for now they are suspended," he said.
The 22,000-strong AMISOM force comprises soldiers drawn from six nations, and has been fighting alongside Somali government troops against the al-Shabab fighers since 2007.
AMISOM donors include the United Nations, European Union, Britain and the United States.
The Human Rights Watch report quoted several women as saying they had gone to the AMISOM camp seeking medicine for their sick babies, but were then forced to have sex.
The vulnerable women largely came from camps in the capital Mogadishu, having fled rural Somalia during a devastating famine in 2011.
African Union chief Nkosazana Dlamini-Zuma has already ordered an investigation into the allegations, and the probe is due to be completed by November 30.
The pan-African bloc, however, has also accused Human Rights Watch of being unfair and inaccurate, and of undermining peace efforts in the war-torn Horn of Africa nation.