Kamal al-Ayoubi was the chargé d'affaires at his country's embassy in London following the departure of its ambassador last year and the expulsion of three other officials in May.
Ayoubi, a Kurd, was not available for comment, but the Foreign Office trumpeted his move – clearly a defection – as "another blow" to the regime of the president, Bashar al-Assad, in the wake of the recent departure of its envoy to Iraq as well as other diplomats and an influential senior Republican Guard commander.
In Syria itself the deputy police chief in the coastal city of Latakia, a stronghold of Assad's Alawite clan, was among 12 officers who fled across the border to Turkey. Fighting also continued between rebels and government forces in and round Aleppo, the country's second city. The UN said 200,000 people had fled it and surrounding areas in the past two days. Many face shortages of food and medical supplies and power cuts.
"It is not known how many people remain trapped in places where fighting continues today," Lady Amos, the UN humanitarian chief, told reporters in New York. "I call on all parties to the fighting to ensure that they do not target civilians and that they allow humanitarian organisations safe access."
The convoy of Lieutenant General Babacar Gaye, the head of the UN observer mission in Syria, was attacked by government forces over the weekend, the UN secretary general, Ban Ki-moon, said on Monday. He told reporters in New York that only the vehicles' armour had protected them from injury.
Al-Jazeera TV said its correspondent Omar Khashram had been injured by shrapnel while covering the Aleppo fighting and evacuated to Turkey for medical treatment.
On the scale of the problems facing Assad, Ayoubi's defection is a minor blow but will add to the sense that Syria's government is in slow-motion collapse. Syria's ambassador to the UK, Sami al-Khiyami, was recalled to Damascus last year as bilateral relations deteriorated. Three more diplomats were expelled at the end of May after the Syrian government was accused of massacring more than 100 civilians at Houla.
"His departure is another blow to the Assad regime," the FCO said in a statement. "It illustrates the revulsion and despair the regime's actions are provoking amongst Syrians from all walks of life, inside the country and abroad."
It added: "We urge others around Bashar al-Assad to follow Mr al-Ayoubi's example, to disassociate themselves from the crimes being committed against the Syrian people and to support a peaceful and free future for Syria."
Ayoubi is said to have informed the Foreign Office of his plans a few days ago. British officials insisted they had not instigated the defection. Five Syrian diplomats now remain at the embassy in London's Belgrave Square, although Ayoubi, a second secretary, was the most senior of them. "We were all shocked when we heard the news," said a colleague. "He was the last person you would have thought would do this. It's just a case of a rat deserting the sinking ship."
Britain's embassy in Damascus is closed, its staff relocated to Beirut.
It is understood that Ayoubi will be eligible for political asylum in Britain on the grounds that he could face persecution if he was to return to his home country. Members of his extended family still live in Syria.
Outside Aleppo, meanwhile, the commander of local Free Syrian Army (FSA) rebel forces confirmed that his troops had seized a key checkpoint north-west of the city early on Monday. "It was a successful operation," Colonel Abdel Nasser told the Guardian. "We took eight tanks and 10 armoured vehicles, as well as mortars and lots of weapons. We also took prisoners." One of his fighters was killed.
Nasser said the Syrian army had responded to the defeat with "light shelling" on Hryatan and neighbouring Anadan, the FSA's previous forward position. "We expect more shelling tonight," he said.
The capture of the Anadan checkpoint is a major boost for the rebels, who now control a land corridor in northern Syria from Turkey all the way to Aleppo's outskirts. Another FSA officer said the route would be useful for resupplying FSA fighters inside the city – and as a haven for refugees seeking to flee.
It also bolsters opposition claims that the rebels are now encircling government forces rather than the other way round. The Assad regime still has 100 tanks and 400 armoured vehicles inside Aleppo. But Nasser suggested government forces were now defending their positions in the centre of the city.
Prospects for diplomatic movement on Syria look slim to non-existent, though David Cameron is to raise the impasse with the Russian president, Vladimir Putin, when they meet in London on Wednesday.
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