Residents said the restaurant was frequented by members of the national security forces, Reuters reported.
There was no immediate claim of responsibility but al-Qaeda-linked al-Shabab militant group has launched many similar attacks in Mogadishu in the past in its bid to topple the government.
"A suicide car bomb rammed into Blue Sky restaurant," police Major Abdikadir Hussein said shortly after the blast.
Abdifatah Omar, a spokesman for Mogadishu's local government, said at the scene that three people had been confirmed dead so far and four others were injured. "The investigation for further details continues," he said.