Somalia's weak, UN-backed government has refused to travel to Sudan for Saturday's peace talks with Islamists who control the capital, Mogadishu.
The president accused the Union of Islamic Courts (UIC) of breaking a truce agreed at the last Sudan talks.
Correspondents say this is a setback for attempts to avoid a confrontation between the two groups.
The UIC delegation has, however, travelled on the first flight to leave Mogadishu's main airport for 11 years.
"We were invited by the Arab League and we are going to attend Khartoum talks. If the transitional government doesn't come, then the international community will see it who wants peace in Somalia and who doesn't," said one of the UIC leaders, Sheikh Sharif Sheikh Ahmed.
Instability had prevented flights to and from Mogadishu's airport until the UIC took control of it last week.
In another sign of increasing tension, interim President Abdullahi Yusuf has again accused the UIC of being backed by foreign Islamic fighters.
Meanwhile, the United Nations Security Council has said it is ready to lift an arms embargo and back a peacekeeping team.
The arms embargo, imposed at the start of Somalia's civil war, would have to be lifted to allow peacekeepers to be deployed and to allow the government to build its own security forces.
The Islamists strongly oppose foreign peacekeepers, which the government says are needed to ensure security.
President Yusuf accused the UIC of becoming more radical and planning to attack his base in Baidoa, 200km from the capital.
"I don't see the use of meeting them in Khartoum again," he told MPs on Friday.
"We will find better solutions, I don't see the value of meeting warriors.
"Our own intelligence sources have confirmed that foreign fighters most of them from the neighbouring Ethiopia, Turks, Afghans and Arabs actively engaged in recent clashes, fighting along the Islamic courts," he said.
The Ethiopians are understood to be ethnic Oromo rebels - the UIC has accused the Ethiopian government of sending troops to support Mr Yusuf in Baidoa.
These claims are rejected by both governments.
The government earlier this week said it would not hold talks with hardline elements of the UIC, saying they were linked to al-Qaeda.
UIC leaders deny the accusations that they are linked to al-Qaeda and have foreign fighters with them.
Earlier this week, the Islamists tightened their grip on Mogadishu and much of southern Somalia by driving one of the last remaining warlords from the city.
Abdi Qeybdid fled to Baidoa and has held talks with interim Mr Yusuf but it is not clear what was discussed.
In Jowhar, UIC authorities have released from prison at least 40 people arrested during protests over the imposition of new taxes.
One person was shot dead during Wednesday's protests.
This is the first time the UIC has tried to impose taxes in the areas it has taken control of in rapid advances during the past two months.
Somalia has not had an effective national government in 15 years.