Moussa Koussa says he is no longer willing to represent the regime in a morale boost for the rebels

Muammar Gaddafi's authority inside Libya suffered a significant blow when his foreign minister quit and fled to the UK in a specially arranged flight organised by the British intelligence services.

Moussa Koussa, who was one of the Libyan leader's closest allies, arrived on a chartered plane from Tunisia and said he was "no longer willing" to represent the dictator's regime.

"We can confirm that Moussa Koussa arrived at Farnborough airport on 30 March from Tunisia," a Foreign Office spokesman said.

Koussa's defection provides Britain with a figure of unparalleled intelligence value in terms of understanding the situation within Gaddafi's inner circle. The move also provides a morale boost to the disorganised rebel forces who have again suffered major reverses at the hands of pro-Gaddafi forces in the past 48 hours.

The Foreign Office said last night: "He travelled here under his own free will. He has told us that he is resigning his post. We are discussing this with him and we will release further detail in due course.

"Moussa Koussa is one of the most senior figures in Gaddafi's government and his role was to represent the regime internationally – something that he is no longer willing to do."

Koussa's defection will be seen as a vindication of the coalition's efforts to intimidate key members of the regime by warning them that if they do not defect they will be taken to the international criminal court to face war crimes trials.

News of the defection first emerged after the official Tunisian news agency reported rumours that Koussa had crossed the border into Libya's western neighbour, but without any clear indication of his motives. The Libyan government, possibly misled by Koussa, said he had left the country on a diplomatic mission for Gaddafi, but the foreign office then disputed this account.

Britain and the US have been in regular contact with him in recent days, mainly through intelligence sources. Probably more than any other senior official inside the Libyan regime, Koussa is seen as the key figure who persuaded Gaddafi to make a deal with British intelligence agencies to stop developing weapons of mass destruction in return for the ending of its pariah status.

However, his relationship with Britain in the past has been far from convivial. Koussa has previously been seen as one of the controlling forces behind the Lockerbie bombing and it was not clear whether he was seeking political asylum.

In 1980, he was expelled from the UK and, for 15 years, he was head of Libyan foreign intelligence – including in the period of the Lockerbie bombing. He has always denied Libya was involved in the bombing.

The Foreign Office added: "We encourage those around Gaddafi to abandon him and embrace a better future for Libya that allows political transition and real reform that meets the aspirations of the Libyan people."

"He has defected from the regime," said Noman Benotman, a friend of Koussa and senior analyst at Britain's Quilliam thinktank.

"He wasn't happy at all. He doesn't support the government attacks on civilians," he said.

"He's seeking refuge in Britain and hopes he will be treated well," Benotman said.

Koussa's decision to abandon the regime came as it emerged that Barack Obama had signed a secret government order authorising covert US help to the Libyan rebels via such organisations as the CIA.

The order, known as a "finding" was signed within the last two or three weeks. The move will undoubtedly fuel speculation that the US and its allies are planning to arm the rebels.

The New York Times has reported that small groups of CIA operatives have been working in Libya for several weeks gathering intelligence for military air strikes and making contacts with the rebels battling Gaddafi's forces, according to American officials. It also reported that "dozens" of British agents and special forces were also inside Libya, helping direct attacks by British aircraft.

Both sides in the Libya conflict are running short of weapons and ammunition after almost two weeks of intense fighting that has brutally exposed the military shortcomings of the rebels, the Guardian has been told.

The rebels were forced into yet another retreat on Wednesday, with Gaddafi's forces regaining much of the territory taken by the rebels at the weekend and threatening to humiliate the western coalition by again coming within striking distance of the city of Benghazi.

Concern is deepening in the coalition about the rebels' fragile morale and lack of military experience to mount a sustained challenge to the regime. A military stalemate is now a real possibility, partly as both sides are struggling to re-equip their forces.

With fighting continuing in Misrata and regime forces pushing east as far as the strategic town of Ajdabiya, the issue of rearming has become paramount.

Coalition bombing raids had helped "chop the legs off" Gaddafi's supply chain, meaning he could no longer get rockets and ammunition to the front line.

"Ammunition is going to become an issue," said a defence source. "The regime's logistics are very stretched. Their ability to move ammunition 400 to 500 miles is becoming constraining. Regime forces have been seriously degraded. But there is more to do to prevent more bloodshed, to prevent more loss of life."

While the regime is thought to be "hurting more and missing more" because many of its heavy weapons have been destroyed, the rebels could struggle to take advantage because of their own problems. They do not have a supply chain or logistical mechanisms.

Many of the rebels have not experienced being under fire before the last three weeks and there is no sign of any improvement in their fighting capability.

Though the US secretary of state, Hillary Clinton, and British foreign secretary William Hague have hinted that arming the rebels might be allowed under the terms of the two UN resolutions, it is understood the UK has not provided any equipment so far, and there are no plans to do so. No training has been provided either.

A defence source insisted there had been "no request for ground forces" and that the coalition had "no intention" of providing them. People who had returned to Ajdabiya after it fell to the revolutionaries on Saturday again fled on Wednesday as the government's army seized two important oil towns further along the coastal highway – Ras Lanuf and Brega.

It was not immediately clear if the regime intended to try to take Ajdabiya again after air strikes last week destroyed a significant number of tanks and armoured vehicles. But the government has pressed ahead with its counter-offensive using not only the artillery that it still retains but what appears to be a larger ground force than previously deployed.

On Monday, the rebels moved within 45 miles (72km) of Sirte, the strategically and politically important birthplace of Gaddafi, and were proclaiming they would be in Tripoli before the end of the week after advancing about 200 miles in two days under the cover of the western air strikes.

But the regime's counterattack has outmanoeuvred the poorly disciplined and ill-trained rebels who barely made a stand at Brega before fleeing toward Ajdabiya. If the government were to move on Ajdabiya, that would once again open the road to Benghazi.

The revolutionary leadership, which has called for an intensification of air strikes, said it was not concerned by the see-sawing military fortunes. "Whether we advance 50km or retreat 50km … it's a big country. They will go back the next day," said spokesman Mustafa Gheriani in Benghazi. But the situation has raised concerns that the rebels' inability to hold territory will undermine coalition commitment.

The coalition now believes it has a much clearer idea of the strengths and weaknesses of the two sides and the issues that could be crucial in the coming days and weeks. It is now thought that:

• Thousands of foreign fighters are in Libya helping to support Gaddafi and more are still coming from countries such as Chad, Niger and Mali. Many are being lured to Tripoli because Gaddafi pays them well. The foreigners, some of them migrant workers, are being used for security in urban areas, freeing up other soldiers to fight the rebels.

• Misrata has become a crucible of the fighting and is the focus of the regime's attempts to snuff out the opposition. Coalition air strikes have crushed attempts by Gaddafi's navy to blockade the city and attack it from the sea. Four Libyan vessels have been sunk, and one beached.

• Al-Qaida has a negligible presence in Libya and is not considered a factor at all in the current fighting.

• Gaddafi has no chemical weapons in any usable form. It is thought that he only has the remnants of the weapons programme that was dismantled in 2004, and coalition air strikes have targeted the Scud missiles that could have been used to deliver them.

How the conflict now develops may depend on whether Gaddafi's opponents in the west of the country are prepared to rise up against a regime that has promoted a culture of fear for the last 40 years.

That culture is thought to be most acute inside the regime itself – Gaddafi is said to hold his lieutenants, extended family, and indeed his children in a state of near perpetual conflict and fear. The default position in society is assessed to be that any resistance to Gaddafi or his regime is something only talked about in the privacy of your own home.

The scale of the deployment by UK forces has also become clear. Ten Typhoon and eight Tornado aircraft are operating out of Italy, supported by the cruise missile submarine, HMS Turbulent, which has been replaced by HMS Triumph.

Getting equipment and armaments to the Mediterranean involved 24 transport aircraft, including nine C17s and 11 Hercules aircraft, and two chartered Antonov flights for 583 military personnel. The RAF so far has undertaken 130 hours of refuelling missions, involving 500,000 litres of aviation fuel.

Key defections

• Interior minister General Abdel ­Fattah Younes al-Abidi, who was considered No 2 in the regime, resigned last month. After nearly 50 years of friendship and service, Abidi admitted that Gaddafi may actually be mad, saying: "He takes very dangerous decisions in a state of anger. It is impossible to think he is completely sane."

• Ambassador to the UN, Abdurrahman Shalgam, an ally of Gaddafi since they were teenage radicals in the 1950s, resigned on 25 February and compared the leader's actions to those of Pol Pot and Hitler. He said Gaddafi had lost the support of 90% of his diplomats.

• The country's ambassador to ­India, Ali al-Essaw, resigned over the ­crackdown on civilians on 21 ­February. He expressed concerns African ­mercenaries were being employed by Gaddafi to attack civilians.

Rowenna Davis