Abdel-Moneim al-Horr, spokesman for the Libyan security committee, said Col. Jumaa al-Kadiki died of wounds from the explosion on a main street in Benghazi.
Al-Horr said another intelligence officer traveling with al-Kadiki was seriously injured.
It was not clear if the bomb was attached to the vehicle or thrown at it. Al-Horr said it was an assassination attempt.
Both officers served under the former regime led by longtime dictator Moammar Gadhafi.
The Sunday blast was the latest in a series against security officials affiliated with the previous regime. The civil war that ousted Gadhafi last year started in Benghazi.