Yusuf on Tuesday denied claims of Ethiopian incursion and called for a deployment of peacekeepers to check the Islamist militia.
After holding talks with his ally Meles Zenawi, the Ethiopian prime minister, in Addis Ababa, Yusuf said Ethiopia had not sent soldiers to support him and that the Islamists were plotting to seize the whole country.
Yusuf also demanded that the Islamic Courts Union give up some of the territory they have captured from Somali commanders before negotiations can take place.
During a meeting with Patrick Mazimhaka, deputy chairman of the African Union Commission, Yusuf suggested that the Islamic Courts' military success may have been helped by Muslim fighters.
"Yes, the Islamists' forces have an international reach and they have many collaborators from around the world ... . They are by the thousands," Yusuf said on Tuesday.
"They could not have overtaken Mogadishu if they did not have the backing of extremists from around the world."
The Somali president was meeting African Union officials to ask for a peacekeeping force for Somalia. He said a UN arms embargo, brought in after opposition leaders ousted Somali leader Mohamed Siad Barre, was complicating efforts to bring in peacekeepers.
Uganda and Sudan were expected to send the first contingent of peacekeepers under the banner of East Africa's seven-nation Intergovernmental Authority on Development.
Major Felix Kulayigye, Uganda's defence spokesman, said that the country plans to send soldiers only after warring factions sign a peace agreement.
Yusuf (R): Islamist fighters may
have been backed by extremists
"Uganda has been ready to send troops to Somalia since last year, but conditions on the ground are not suitable for peacekeeping," Kulayigye said.
"Since the warlords have not yet agreed to a ceasefire, there is no peace to keep."
The leader of the Islamist group, Sheikh Sharif Sheikh Ahmed, has said they will not begin talks with the government while it continues to press for peacekeepers to be deployed in Somalia.
The UN said it will send a security team to meet the leaders of the Islamic courts union. The UN initiative is intended to assess the situation in advance of a visit by humanitarian agencies that want to increase aid to the country, Francois Lonseny Fall, the UN special representative for Somalia, said on Monday.
No Ethiopian troops
Meanwhile, the US has said it had seen no signs of an Ethiopian force on Somali territory and called for the two sides not to "inflame" tensions in the region.
The Islamic Courts Union had called for international powers to pressure Ethiopia to withdraw troops from Somali territory.
"We've seen the reports of Ethiopian troop movements on the border," said Adam Ereli, a state department spokesman.
"We've talked to the Ethiopian government about it. We have seen no evidence of incursions."
"We think that all parties in the region need to act responsibly and not take steps to further destabilise or inflame the situation."
Muslim clerics in Somalia said several hundred Ethiopian soldiers had crossed into Somalia at the weekend and were moving towards the headquarters of the Somali transitional government in Baidoa, about 250km from the Mogadishu.