Bondhere District Commissioner Zeinab Yusuf told reporters that the Saturday incident in Bondhere district saw a remote-controlled explosive device go off, resulting in the death of the National Intelligence Service Agency (NISA) official.
"Security forces have arrested several suspects following the blast," Yusuf said, noting that the victims were people of the same family except a passer-by woman who was injured.
"An explosive device fitted into the vehicle caused the blast and he died on the spot," the commissioner said.
The security forces have not established why the improvised device was fitted in the car with the civilians onboard but sources said a senior police officer who is believed to have been the target escaped unhurt.
Security officials told Xinhua that the official was carrying his family to the Mogadishu Airport. Witnesses reported the blast was huge and caused panic in the area.
"We heard huge blast this morning and we learnt that it had targeted security official. Heavily armed forces arrived at the scene and arrested some people," an eyewitness, Amina Abdullahi, told Xinhua.
No group has claimed reasonability for the latest attack but the extremist al-Shabab military group launches regular attacks on government, military and civilian targets in Somalia.
The latest attack comes a week after two people were killed when a suicide car bomb detonated at the checkpoint, which is close to the presidential palace.