(Adds Somali Prime Minister's reaction)
By Yara Bayoumy and Elias Biryabarema
KAMPALA/MOGADISHU, Nov 3 (Reuters) - Somalia's prime minister said on Saturday that it could be a challenge for his country if Uganda followed through on a threat to withdraw troops fighting Islamist rebels in southern Somalia.
Uganda's foreign affairs ministry said earlier that it would withdraw from peace keeping initiatives in Africa unless the United Nations amended a report accusing it of supporting rebels in the Democratic Republic of Congo.
Somali Prime Minister Abdi Farah Shirdon Saaid told Reuters in an interview that Somalia had not yet received any official communication from Uganda on the issue of withdrawing from the African Union force known as AMISOM.
"We are not impressed with that message. We would like to work with AMISOM in that respect," he said.
"The Ugandans have contributed significantly and a lot, and this is now a critical moment and in light of that we are of the view, if the media reports turn out to be true, it may be a challenge."
Stung by accusations of support for Congo's M23 rebel group, Uganda's security minister said on Friday Kampala would tell the United Nations it was withdrawing its forces from military operations in Somalia and other regional hotspots.
Uganda and its neighbour Rwanda have denied accusations contained in a leaked report by a U.N. Group of Experts that the two countries have helped the M23 rebels, whose warlord leader has been indicted by the International Criminal Court.
"Uganda's withdrawal from regional peace efforts, including Somalia, CAR (Central African Republic) etc would become inevitable unless the U.N. corrects the false accusations made against Uganda, by bringing out the truth about Uganda's role in the current regional efforts," the foreign ministry said in a statement.
U.N. diplomats in New York said it was unclear whether Uganda meant the threats seriously or was merely trying to pressure Security Council members from taking action on the Group of Experts' recommendations.
The experts called for U.N. sanctions against individuals supporting the M23 rebels.
Troops from the Uganda People's Defence Forces (UPDF) account for more than a third of the 17,600 U.N.-mandated African peacekeepers fighting Islamist al Shabaab rebels in Somalia and their withdrawal could hand an advantage to the militants, who are linked to al Qaeda.
A sudden reduction in peacekeeping numbers, especially in the capital Mogadishu, would risk undoing the security gains that allowed the first presidential elections in decades to be held in the capital in September.
Uganda's soldiers, backed by U.S. special forces, are also leading the hunt for fugitive Ugandan warlord Joseph Kony in Central African Republic, with some stationed in South Sudan.
A Nairobi-based diplomat told Reuters it was unlikely Uganda would pull back its troops.
"Uganda plays a key role in AMISOM and has invested a lot. The international community has supported the UPDF and it would be difficult at this stage, at least in the short term, to take a step back," the diplomat said. (Reporting by Justin Dralaze and Elias Biryabarema in Kampala; Yara Bayoumy in Mogadishu; Writing by George Obulutsa)