"About 80 per cent of Somalia is not safe and is not under control of the government," Sheikh Qasim told The Associated Press.
"Islamists are planning to launch a massive attack against the [government] and its allied troops."
He appealed for international support, saying the fighters "are everywhere".
Somali government officials have rarely acknowledged what many observers have concluded about their tenuous grip on power.
But on Thursday, presidential spokesman Hussein Mohamed Mohamud confirmed that the fighters were regrouping with "a lot of weapons and foreign fighters".
Last year the Ethiopian military provided military back-up for the government to drive the Islamic Courts fighters out of Mogadishu, which they had held for six months along with the south of the country.
Ted Dagne, an African specialist for the research arm of the US congress, said the group was never truly gone, simply underground.
"The Somali and Ethiopian governments may have underestimated the level of organisation and determination on the part of the Islamic Courts," he said.
He added that many people look back on the group's six months in power and conclude the country then "was relatively peaceful and gave hope to the people of Somalia that after over a decade of violence, they can live in peace".
But Ethiopian officials deny the group's resurgence.
"The facts on the ground tell you that they are in bad shape and having serious difficulties," said Bereket Simon, an adviser to Meles Zenawi, Ethiopia's prime minister.
Outside Mogadishu, members of the group and its Shabab military wing have been spotted with increasing frequency throughout central Somalia where before they had been hiding.
In Kismayo, Somalia's third-largest city, a member of the Shabab said his group was sending soldiers to the capital 500km away to fight the Ethiopians daily.
Fighting between the Islamic Courts Union and the Ethiopian-backed interim government has killed nearly 6,000 civilians in Mogadishu this year alone, according to a local human rights group.
More than 700,000 people have been displaced, leading the UN to call Somalia's humanitarian crisis the worst in Africa.
The bloody nature of the conflict was highlighted once more on Thursday when mortars slammed into the biggest market in Mogadishu killing at least 13 people and wounding more than 40, while a separate gun battle killed five people.
The market in Mogadishu's Bakra district was packed with shoppers preparing for the weekend when the attack occurred and the toll is expected to rise.
There has been no effective government in the country since 1991 when tribal commanders overthrew Mohammed Siad Barre, the president, then turned on one another.
The current interim government was formed in 2004 with the support of the UN, but has struggled to assert any real control.
About 1,800 Ugandan peacekeepers are in Somalia, officially as the vanguard of a larger African Union peacekeeping force, although no other countries have sent reinforcements so far.
|Fighting in Somalia has killed nearly 6,000 civilians and displaced 700,000, making |
it Africa's worst humanitarian crisis, according to the UN [AFP]