Libyan intelligence agency buildings were also attacked in the overnight raids on Tripoli, using Tornado aircraft and Tomahawk missiles fired from the submarine, HMS Triumph.
One of the intelligence centres hit played a "significant role in the collection of information by Colonel Gaddafi's secret police", and the other was a headquarters for Libya's External Security Organisation, the ministry said.
Libyan officials summoned reporters after the attack in the early hours to visit the two damaged buildings, which they said housed internal security forces and Libya's anti-corruption agency. One building was in flames.
The targets appeared to indicate a broadening of British operations, which until now have concentrated on knocking out Libyan weapons and command and control systems.
Britain's most senior military officer, General David Richards, said at the weekend that Nato must broaden its range of targets in Libya or run the risk of Col Gaddafi staying in power.
Nato officials said there had been no change in the rules of engagement agreed by all 28 Nato allies and that all alliance strikes had been aimed at military targets.
"We have been consistently striking military targets … We will continue to keep up the pressure until the military goals have been met," Nato spokeswoman Oana Lungescu said.
Military spokesman Wing Commander Mike Bracken said Nato strikes had hit a broad range of targets in the past four days.
He said the situation in Brega was now stable, although there was sporadic fighting between pro- and anti-Gaddafi forces away from the town and the civ-ilian population. Nato had also relieved pressure on the rebel-held town of Misrata.
"Misrata is much safer than it was even a few days ago with less shelling on the city," he said.
"The western villages are holding on and we continue to attack pro-Gaddafi forces that threaten civilian populations," Wing Cmdr Bracken told a news briefing.
"We are achieving our objectives of reducing the Gaddafi regime's capacity to co-ordinate strikes against innocent civilians and diminishing its will to fight."
The MoD said the training base that was attacked was used by Col Gaddafi's Executive Protection Force, which acts as the bodyguard for Col Gaddafi's inner circle government and was entrusted with other "sensitive tasks".
Vehicles at the training base had been "identified as having been directly involved in the bloody suppression of public demonstrations in Tripoli on 4 March, when live ammunition was used against the legitimate protesters".
Russia hosted a representative of Col Gaddafi's government in Moscow yesterday and called on Tripoli to stop using force against civilians, comply fully with UN Security Council resolutions and withdraw armed groups from cities.
Russia is keen to act as peacemaker and preserve its influence in Libya, where it has billions of dollars of arms, energy and infrastructure contracts.