The red phone had been silent for more than 20 years, encased in reinforced glass in the corner of the major's office. When it rang just after midnight on 6 September 2007, the startled Syrian officers nearby had to remind themselves what to do.

"I told my colleagues that we had to break the case with a hammer, then answer it," said Abu Mohammed, a former air force major then based at an air defence station near the north-eastern city of Deir Azzor. "It had not even rung during a training exercise."

Abu Mohammed, now a senior member of the rebel movement in the north of the country, broke the glass. What followed, he said, were the most puzzling 10 minutes of his military career.

"I shattered the glass and answered the phone," he said. "There was a brigadier on the other end from the strategic air command in Damascus. He said: 'There are enemy planes approaching, you are not to do anything.'

"I was confused. Do nothing? This is what we were waiting for. We couldn't see them on our radars. And then our radars were jammed. The missile base nearby could not have fired even if it was allowed."

Until last week, the Israeli raid in 2007 that destroyed what the International Atomic Energy Agency concluded was a nuclear reactor at al-Kibbar, north of Deir Azzor, was the last time Syria's much-vaunted air defence system was tested.

But last Wednesday just before dawn, the Israeli planes returned. The attack formations were obvious on the radar systems used by Nato tracking stations and by Lebanese civil aviation: about 10 jets, all of which approached from the Mediterranean over southern Lebanon.

Some of the planes remained circling in Lebanese airspace. Others crossed into Syria, firing eight missiles near a building 11 miles north of Damascus and then flying west. Just like at Deir Azzour six years ago, the Syrian air defences stayed silent.

"They did the same as what they did to us," Abu Mohammed said on Monday from the Aleppo countryside. "The reality is that we are blind in the face of the enemy."

Syrian defence officials have claimed that the invading planes escaped by staying below the radar. Opposition figures, meanwhile, have largely either ignored the attack or pretended it didn't happen. Better that than to acknowledge a sworn enemy of both sides was making things easier for them.

Nearly two withering years of war have clearly taken a toll on the Syrian military, which before the insurrection was reputed to be one of the region's most powerful. Army bases were considered impregnable, air defences the most formidable in the region, and soldiers resolutely loyal.

"The only thing we really still fear is the Migs," said Maalik Sayedi, a carpenter turned guerrilla fighter, as he picked through the remains of an overrun infantry school on the northern outskirts of Aleppo. "When we raided this place, the fight was over in less than two hours."

The infantry school is one of four nearby regime bases overrun between mid-December and late January. Units stationed in this bleak, sprawling complex, which was the main training site in northern Syria for officers and soldiers alike, put up less of a fight than those defending airbases. Signs of the rout are everywhere.

In the middle of a field, surrounded by pine and fir trees, five delapidated Soviet tanks, the defensive core of the inner base, stand in ruin. The maker's plate inside each says 1959. Four armoured personnel carriers are in crumbling disarray, their cables and rusting armour discarded across fields churned muddy brown by tank tracks.

Until December this base was one of the last regime strongholds in northern Syria. But now those who once would not dare approach the giant concrete walls and watch towers that surround it are picking the base clean like a carcass. Anything is fair game, especially wood, which is being harvested from wherever it can be found to heat family homes.

Hundreds of old trees just inside the wall have been sawn down, their stumps exposing buildings that long stood as tribute to the military's position at the heart of Syrian society. The denuding of the perimeter is exposing the base's secrets. And those drifting inside to see them are underwhelmed.

"It was exciting at first," said 17-year-old Hussein Mohammed, carrying a hacksaw in one hand and a plastic bucket full of kindling branches in the other. "But this is it," he said with a wave of the saw. "This is where you learned to be a soldier in the Syrian army."

Vivid murals of the late dictator Hafez al-Assad are painted on walls on the parade grounds and at the base's main entrance, now manned by dozing rebel fighters. Though Bashar al-Assad has run Syria for almost 13 years, he is afforded only one portrait. His late older brother Basil, killed in a car crash in 1994, still takes pride of place next to his father here.

All around are obstacle courses. Hundreds of rusting black and white hoops and bars, and truck tyres half buried in the soil. Whatever their shortcomings, graduates from this school must have been fit.

Later, in the biting cold of a mid-winter night in Aleppo, Firas Tmeimi, who took part in the infantry school raid and has since joined attempts to storm other bases, said each operation was a revelation.

"We thought they were strong. But the veil has been lifted. Fear was the regime's greatest weapon. Without that, we can match them," he said, before stopping in mid sentence as a distant roar drew nearer.

"Except for the planes," he added, ducking as a low-flying jet streaked overhead. "Two of them are worth more than all the airbases we've seized."

• This article was amended on 5 February 2013 to correct the spelling of fir trees, from fur trees.