The AU appeal comes after the UN Security Council on Tuesday failed to agree on a statement calling for ending the war and the withdrawal of foreign troops from Somalia.
Several council members objected to the Qatari-circulated statement's naming of Ethiopian forces in particular.
Meanwhile, Francois Lonseny Fall, the UN secretary-general's special representative to Somalia, said the fighting had forced the UN to evacuate and halt assistance to two million people.
The UN World Food Programme has suspended air operations in Somalia and pulled out its air-support staff, officials said on Wednesday.
Fall of Jowhar
"The government has taken over Jowhar. I can see government troops on top of armoured vehicles chasing Islamists troops ... heading towards Mogadishu," Mahamud Ismail, a resident, said on Wednesday from the town 90km north of the Somali capital.
Residents came out of their houses and cheered pro-government troops, backed by Ethiopian tanks, in pursuit of Islamic Courts fighters as sporadic fire echoed in the air, witnesses said.
A former local commander who ruled Jowhar before it was captured by the Islamic Courts in June led the Somali government troops as they drove into the city, residents said.
"Ethiopian troops and Mohammed Dheere have entered the city," said Abshir Ali Gabre. Others said he was wearing a T-shirt that said "I love Jowhar" as he shook hands with residents.
Fighting could still be heard at a military camp south of the city.
The capture of Jowhar came hours after Ethiopia, defending the Somali interim government, said it was halfway to crushing the militia, heightening fears its next step would be to use air strikes and ground troops to seize the capital.
Troops headed for Jowhar after driving Islamic Courts fighters from Bandiradley, Adadow and Galinsor.
On Tuesday, fighters of Islamic Courts retreated from the main frontline after a week of artillery and mortar fighting.
Security Council statement
The Arab League is expected to hold a meeting on Wednesday with the African Union to discuss the situation in Somalia.
The Islamic Courts fighters appeared to be heeding a call by Sheikh Sharif Ahmed, a senior leader, that forces gather in the capital to prepare for a long war against Ethiopia.
"Most of our troops should converge in and around our bases in Mogadishu and should prepare for a very long war against our enemies," he said late on Tuesday.
The Ethiopian prime minister said that more than 1,000 people have been killed in the fighting.
"We got reports of more than 3,000 wounded in a Mogadishu hospital. Those who died are well over 1,000," Meles Zenawi said, two days after Ethiopia admitted military intervention in the country.
|The Red Cross says thousands of people have |
fled their homes due to the fighting [AFP]
Both sides have reported killing hundreds of their opponents in the recent fighting, but the claims could not be independently confirmed.
The Red Cross said that more than 800 casualties had been admitted to hospital since the fighting began and thousands of people had fled their homes.
The Islamic Courts admitted that they had been forced to withdraw from many frontline positions, but have vowed to dig in for a long war with Ethiopia, which has denied intentions of taking the capital.
"Liberating towns is not our agenda. Our troops have not entered any town," Meles said.
"Our forces and that of the [transitional federal government] have broken the back of the international terrorist forces around Baidoa and they are in full retreat now."
Heading for Mogadishu Abdelkarin Farah, Somalia's ambassador to Ethiopia, said in Addis Ababa on Tuesday that the transitional government's forces were 100km from the capital.
Islamic Courts fighters withdrew more than 80km to the southeast from Daynuney, a town just south of Baidoa and advancing government and Ethiopian troops captured Bur Haqaba, one of the Islamic Courts' main bases, after it was abandoned early on Tuesday.
"We woke up from our sleep this morning and the town was empty of troops, not a single Islamic fighter," Ibrahim Mohamed Aden, a resident of Bur Haqaba, said.