At least 12 people were killed and about 30 others were wounded on Thursday in fighting between fighters loyal to the Islamist courts and militias linked to the secular regional commanders' alliance based in Sisi district, the correspondent said.
AP reported that at least 48 people were dead and thousands of frightened civilians had run away from their homes.
Witnesses said mortars and bullets were flying in various parts of south Mogadishu.
Witnesses also said that the fighting spread across the Somali capital from its northern end, which had been the scene of fierce battles in recent weeks.
Muslim militiamen from the Islamic Courts Union made a rare foray into southern and eastern parts of Mogadishu and captured a strategic road junction in the centre of the city, known as K4.
They also seized the historic Sahafi Hotel, which is owned by a member of the secular alliance known as the Alliance for the Restoration of Peace and Counterterrorism.
Residents said on Thursday that this was the first time since 1992 that battles had taken place in different parts of Mogadishu on the same day.
Dr Abdi Ibrahim Jiya of the Somali Doctors Association said that at least 48 people died in the fighting, citing information the association collected from Mogadishu's main hospitals.
"I have never seen such a heavy exchange. Mogadishu is blazing with fire"
secular coalition member
Jiya said that about 90 people were injured, but casualty tolls were likely to rise because many civilians were unable to make it to a hospital.
Thousands of civilians fled their homes on foot, some with children on their backs, trying to keep from being caught in the crossfire or struck by stray rockets, shells and bullets.
Both sides confirmed the fighting. Ibrahim Maalim, a secular coalition member, described the fighting as very heavy.
"They are hitting each other with mortars, anti-aircraft missiles and anti-tanks.
"I have never seen such a heavy exchange. Mogadishu is blazing with fire," Maalim said.
As he spoke to Reuters, heavy artillery and gunshots reverberated over the telephone.
He said: "There are bodies lying everywhere. I cannot count them and there are wounded people lying on the streets crying for help."
Witnesses said they saw Muslim militiamen set ablaze a secular coalition vehicle. Others saw the bodies of three Muslim fighters on a pick-up armed with heavy guns.