"Obviously, when there's instability anywhere in the world, we're concerned. There is instability in Somalia," George Bush said on Tuesday.
"The first concern, of course, would be to make sure that Somalia does not become an al-Qaeda safe haven, it doesn't become a place from which terrorists can plot and plan.
"And so we are watching very carefully the developments there, and we will strategise more when I get back to Washington as to how to best respond to the latest incident there in Somalia."
But on Wednesday, a leader of the Somali Islamist group that claimed to have taken control of Mogadishu said Bush's concerns about terrorism were unfounded.
Shaikh Sharif Shaikh Ahmad, the head of the Islamic Courts Union, told Aljazeera that "there is no terrorism in Somalia". He said: "We have no connection to terrorism."
Shaikh Ahmad: Somalis have the
right to run their own country
Armed men loyal to the Alliance for the Restoration of Peace and Counterterrorism, said to be funded by the US, faced the courts union in a stand-off in Somalia on Tuesday after the courts militia claimed control of the capital.
Ahmad said Bush's statements came as a result of the defeat of the alliance.
"Somalis have the right to choose what they want and run their country," he said. "America should consider the will of the Somali people."
Ahmad said that "Islamic courts are nothing more but popular organisations which were formed for special missions".
They have no aggressive intentions against any country".
Asked about talk of the establishment of an Islamic state, Ahmad said: "We are Muslims and the Somali people have the right to choose what they want.
"There is no terrorism in Somalia. We have no connection to terrorism.
Somalis have the right to choose what they want and run their country"
Shaikh Sharif Shaikh Ahmad,
head of the Islamic courts
"We at the Islamic courts would not force on Somalis anything they do not want."
Ahmad said that "the US should clear up its opinion of Islam".
"It has linked the word terrorism to Islam and this is wrong."
A day after the Islamists declared victory after four months of battles with the alliance, Mogadishu was fractured along clan lines. Remaining regional commanders said they would not bow to demands to surrender.
The two camps held rival rallies in the city as hundreds of Islamic courts fighters camped outside the regional commanders' last stronghold of Jowhar, about 90km north of Mogadishu, awaiting orders to attack the town, witnesses said.
The regional commanders' alliance was created in February with US support in an attempt to curb the growing influence of the Islamic courts.
Somalis attended rival rallies
in Mogadishu on Tuesday
Washington has never publicly confirmed or denied its support for the alliance, but US officials told AFP that they had given the regional commanders money and intelligence to help to rein in "creeping Talibanisation" in Somalia.
On Tuesday, Sean McCormack, the state department spokesman, said Washington was not destablising Somalia by supporting regional commanders. He said it needed to fight the presence of al-Qaeda in the east African country.
McCormack said: "We certainly want to work with people in Somalia who are interested in combating terrorism. The presence of foreign terrorists in Somalia is a destabilising fact."