The Ugandan soldiers arrived in Somalia after the African Union made an urgent appeal on Wednesday for the mission funding.
As with its previous peacekeeping foray in Sudan's violent Darfur region, the AU is facing a shortage of money and equipment for its Somalia assignment.
The amount of money pledged for the six month operation - mainly from the European Union and the United States - falls well short of the estimated cost.
"We are running out of time," Bering Mtimkulu, head of the AU's peace support operation division, said.
"We need urgent assistance from the international community to help us expedite the deployment of the AU peace force in Somalia."
The European Union said in January that it was only prepared to contribute if Abdullahi Yusuf, the Somali president, took steps towards reconciliation in the deeply divided country.
And, on Thursday, Yusuf announced that a national reconciliation conference in Mogadishu would begin on April 16 and last for two months.
"There will be 3,000 participants from outside and inside the country," he told the Somali parliament.
"The favour of Western countries is vital to Somalia's future"
Angus Hogg, Horsham, UK
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The Islamic courts has threatened to carry out suicide attacks against the African peacekeepers.
Yoweri Museveni, the Ugandan president, has said his troops will not try to disarm groups of fighters in Mogadishu.
"We are not going to disarm the Somali militias because if we empower the Somali people, it will be up to them to decide whether it is necessary to disarm," Museveni told a gathering troops due to leave for Somalia.
"We don't go to Somalia to impose peace on the Somali people, but to help empower them to rebuild their country and help them to rebuild their army. That is our line of responsibility," he said.
The United Nations Security Council approved the deployment of the AU force in a unanimous vote on February 20.
The force will have to confront growing violence in Mogadishu which has seen a rise in insurgent attacks and fighting since Somali government fighters backed by the Ethiopian military ousted a powerful Islamist movement late last year.
So far, the AU has managed to raise only around half of the required 8,000 troops.
Uganda has offered 1,500 troops, Burundi 1,700 and Nigeria 850, while Malawi and Ghana are also expected to contribute.
The under-equipped and cash-strapped African force will have to patrol a country, home to some 10 million people, that has been in anarchy and carved up among rival clans since the 1991 ouster of president Mohamed Siad Barre.