Medical workers said at least 20 people were killed in fighting on Thursday, while the toll from Wednesday rose to 40 after families took their wounded to hospitals after clashes subsided at night.
They cited figures gathered from hospitals in Mogadishu by the city's doctors' association.
Earlier, Wednesday's toll had been estimated at 20. Among the dead were civilians caught in the crossfire.
Residents said that sporadic gunshots that began early on Thursday escalated into heavier fighting later in the day, with the sound of exploding mortars and gunfire ringing in north-eastern Mogadishu.
Witnesses and medical sources said the clashes were sparked on Wednesday when armed men allied to Bashir Raghe Shiral, a member of the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT) and rival fighters who back Abukar Omar Adan of the Islamic courts clashed over land ownership.
Both sides used rocket-propelled grenades, anti-aircraft guns, machine guns, assault rifles and hand grenades. Dozens of people fled their homes.
The violence was the result of a unresolved dispute over ownership of a piece of land near Aisaley airport, some 30km north of Mogadishu, according to an ARPCT member.
The ARPCT, a coalition of warlords which was formed last month, is aimed at curbing the influence of Islamic extremism in Somalia, while the Islamic militia say they want to maintain law and order.
Witnesses said that there was sporadic gunfire on Thursday although the intensity was less. There were no immediate reports of injuries.
At least 33 people were killed, hundreds wounded and thousands displaced when similar groups clashed in southern Mogadishu last month.
Somalia has been wracked by chronic unrest with warlords and rival militias fighting for control of unruly fiefdoms since the 1991 overthrow of dictator Mohamed Siad Barre.