Nearly 70 people remain missing, and 295 still have injuries suffered in the attack, Abdullahi Mohamed Shirwac, the chairman of the 11-member government investigation committee, said in a press conference.
The October 14 attack was already the deadliest in Somalia's modern history. Government officials reported the death toll at 358 near the end of October. Two Americans were killed in the blast, the US State Department said.
It was not immediately clear what caused the death toll to increase so significantly more than a month and a half after the deadly attack. There still has been no claim of responsibility.
The initial vehicle bomb destroyed dozens of stalls and the popular Safari Hotel in the heart of the city. Minutes later, a second vehicle bomb went off nearby.
One truck was packed with explosives, including cooking gas. The force of the blast was the worst Somalia has seen in at least 10 years, CNN correspondent Farai Sevenzo reported.
Michael Keating, special representative of the United Nations secretary-general for Somalia, said whoever was behind the "revolting" attack "killed an unprecedented number of civilians."
Rescue workers had to comb through piles of rubble to try to locate victims. Those with serious wounds were airlifted for treatment to Turkey, Sudan, and Kenya. Mass burials took place as President Mohamed Abdullahi Farmajo called for three days of national mourning.
Mogadishu, a large city on the east African nation's coast, has endured high levels of violence for years. Al-Shabaab, an al Qaeda-linked terror group, has carried out several deadly bombings.
Al-Shabaab has been waging a war with the Somali government for more than 10 years, prompting the African Union to send in peacekeeping troops. The terror group is now based mainly in rural areas in the south of the country, having lost control of Mogadishu in 2011.
Last August, the US State Department warned Americans to avoid traveling to Somalia because of widespread terrorist and criminal activity. The warning said al-Shabaab and ISIS "operate with relative impunity throughout large parts of the country, including Mogadishu, and attack civilian, military, and government targets."
The White House issued a statement condemning the October attack, calling terrorist organizations "the enemies of all civilized people."