The explosion occurred as vehicles lined up at a checkpoint at Sayidka Junction. The intersection is close to the parliament building and the presidential palace.
Mogadishu ambulance services confirmed the death of three people including an administration and finance officer at the Ministry of Women and Human Rights. In addition, the death of a security officer at the Somali parliament building was confirmed to VOA Somali by authorities.
Medical services say they evacuated 15 injured victims.
The al-Shabab militant group claimed responsibility for the attack.
This is the first major attack by the group in Mogadishu in the New Year and it comes just 12 days after a deadly truck bomb at the main Ex-Control junction, which killed over 80 people.
Also this week, the group attacked a Kenyan military base housing U.S. military personnel, killing three Americans.