Moussa Ibrahim says three of Moamar Gaddafi’s grandsons were also killed but the leader himself was unharmed.
“The house of Saif al-Arab Gaddafi … who is the youngest of the leader’s children, was attacked tonight with full power,” he said.
“The leader with his wife was there in the house with other friends and relatives.”
Saif al-Arab was a civilian and a student who had studied in Germany.
But Mr Ibrahim told a news conference in Tripoli that Moamar Gaddafi himself was not hurt.
“The leader himself is in good health; he wasn’t harmed,” he said.
“His wife is also in good health; she wasn’t harmed [but] other people were injured.
“This was a direct operation to assassinate the leader of this country.”
Mr Ibrahim had earlier taken journalists to the remnants of a house in Tripoli.
Given the level of destruction, it is unclear that anyone could have survived, raising the possibility that if Moamar Gaddafi was there, he had left beforehand.
Three loud explosions were heard in Tripoli on Saturday evening as jets flew overhead.
Volleys of anti-aircraft fire rang out following the first two strikes, which were followed by a third.
The Libyan rebel capital Benghazi was rocked by sustained gunfire and explosions as fighters sent off volleys of celebratory fire after reports of the younger Gaddafi’s death.
“They are so happy that Gaddafi lost his son in an air strike that they are shooting in celebration,” said Colonel Ahmed Omar Bani, military spokesman of the Libyan opposition Transitional Nation Council, headquartered in Benghazi.
An international coalition began carrying out strikes on forces loyal to Moamar Gaddafi on March 19 under a United Nations Security Council mandate to protect Libyan civilians.
NATO took command of operations over Libya on March 31.