Stung by the loss on Wednesday of a key position in northeast Mogadishu, the alliance attacked on Thursday the Islamists at the nearby village of El Arfid, north of the city, sparking a fierce exchange in which three were killed and seven wounded.
"The fighting between Islamic courts and warlords has started in the El Arfid and Dermoley areas," said Moalim Ashi, an elder in the nearby town of Balad, about 30 kilometres from the capital.
More than 500 heavily armed fighters on both sides backed by scores of pick-ups with machineguns mounted on them were involved in the clashes that sent hundreds of villagers fleeing in terror, witnesses said.
"At least three people were killed in today's fighting and seven more were wounded," Abdi Ibrahim, a doctor at the Al-Hikma hospital, told AFP.
The alliance had been regrouping in Balad with reinforcements from the town of Jowhar, some 90 kilometres north of Mogadishu, with an eye to attacking the Islamists.
Witnesses said the fighting had cut roads between the capital and Jowhar.
In Mogadishu itself, sporadic gunfire could be heard around the northeastern neighborhood of Sukahola, where the Islamists seized alliance positions in co-ordinated attacks on Wednesday, residents said.
A day after the two sides pounded each other with heavy machinegun, rocket and artillery fire, the area was tense but generally violence free, although the death toll from Wednesday's clashes rose by three to 10, they said.
"Apart from the sporadic gunfire, Sukahola is relatively calm," said a resident, Abdulahmed Noor, who like others expressed deep concern about a resumption in battles.
"We fear fighting could erupt at anytime because the gunmen have not moved from the frontlines," said another resident, Amina Mohammed.
In addition to three people who died of their wounds overnight, doctors at Al-Hakma hospital, citing militia sources, said another three fighters had been killed on Wednesday, bringing that death toll to 13.
The latest fatalities brought to at least 78 the number of people killed in the most recent round of clashes that began last Wednesday, worsened Thursday and exploded on Saturday, when 30 people died.
More than 316 people have been killed and more than 1,500 wounded, many of them civilians, since the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT) and the Islamic courts began battling in February.
Somalia has been without a functioning central authority since 1991 and the country's largely powerless transitional government, based in Baidoa about 250 kilometres (155 miles) northwest of Mogadishu, has blamed the alliance and the United States for the fighting.
The US denies responsibility for the clashes, although it has refused to confirm or deny its support for the ARPCT.
But US officials and Somali analysts have said off the record that Washington has given money to the ARPCT, one of several groups it is working with to curb what it says is a growing threat from radical Islamists in Somalia.