NATO jets hit a target near Libyan leader Muammar Gaddafi's compound in central Tripoli early on Saturday, which the government described as a car park but which Reuters reporters said looked like a bunker.
Government spokesman Mussa Ibrahim said three people were killed by the "very powerful explosion" near Gaddafi's Bab al-Aziziyah compound in the early hours of Saturday.
Reuters reporters said cars were parked on the empty land but the area was surrounded by a wall and guarded by watchtowers and soldiers, suggesting it was not simply wasteland.
They saw two large holes in the ground, where the bombs had torn through a layer of soil, followed by a layer of reinforced concrete, to pierce what appeared to be an underground bunker.
Smoke was rising from one of the craters and ammunition crates lay nearby.
Ibrahim said the area was disused and the ammunition boxes were empty.
Reuters correspondents in Tripoli heard jets fly over the city, and felt a rumbling that shook walls and rattled windows.
Rebels say NATO forces appear to have stepped up attacks on areas controlled by Gaddafi in recent days.