The United States has said it will "reserve judgement" after the Islamist militia in charge of the Somali capital strongly denied supporting terrorism.
A US State Department spokesman said the Union of Islamic Courts was not a "monolithic" group.
The Islamist leader on Wednesday tried to calm western fears by sending a letter to foreign diplomats saying they were not "harbouring any terrorists".
The courts seized Mogadishu from warlords believed to have US backing.
The US has neither confirmed nor denied reports that they supported the Anti-Terror Alliance of warlords.
But on Tuesday, US President George W Bush said he would ensure that Somalia did not become a safe haven for al-Qaeda.
Meanwhile a senior interim minister say he expects the Union of Islamic Courts to eventually join them in government.
The deputy head of the government based in the town of Baidoa, Ismail Mahmoud, said contacts had been taking place.
The transitional government only controls a small part of Somalia, which has not had a functioning national authority for 15 years.
BBC Somali Service editor Yusuf Garaad Omar says the Islamists are generally far more popular than the warlords, who are hated for their role in Somalia's 15-year civil war.
The Islamist militia are now reported to be gathering outside Jowhar, some 90km (58miles) north of the capital, where some of the remaining warlords have fled.
They are reported to have ordered a halt to any flights from the airport there to prevent any warlords fleeing.
The letter to diplomats, signed by Sharif Shaikh Ahmed, said: "We categorically deny and reject any accusation that we are harbouring any terrorists or supporters of terrorism in the areas where the courts operate...
"We share no objectives, goals or methods with groups that sponsor or support terrorism."
Mr Ahmed is seen as a relative moderate, while at least two senior figures are considered to be more radical - Sheikh Hassan Dahir Aweys, who is on the US list of terror suspects, and Afghanistan-trained militia commander Adan Hashi Ayro.
One of the Somali warlords was arrested and deported from Kenya, after it said it would no longer host those who "destabilise" its lawless neighbour.
Abdirashid Shire Ilgayte, a member of the alliance defeated by an Islamic militia in recent fighting, was led from his Nairobi hotel by police.
Kenya has played host to Somali peace talks involving almost all faction leaders, for the past three years.