Dozens of others were injured in the explosion early on Sunday.
The bomber struck at the entrance of the city's main port facilities. Residents say the blast could be heard across Mogadishu.
No group has said it carried out the attack, but the Somali Islamist group al-Shabab often carries out such bombings in the capital.
"We assisted 48 wounded people and carried 16 others who were killed in the blast," said Abdikadir Abdirahman Adem, head Mogadishu's Amin ambulance service.
The death toll is expected to rise further.
A suicide car bomber has killed at least 16 people in the Somali capital Mogadishu, officials say.