Turkey and Saudi Arabia are actively supporting a hardline coalition of Islamist rebels against Bashar al-Assad’s regime that includes al-Qaeda’s affiliate in Syria, in a move that has alarmed Western governments.

The two countries are focusing their backing for the Syrian rebels on the combined Jaish al-Fatah, or the Army of Conquest, a command structure for jihadist groups in Syria that includes Jabhat al-Nusra, an extremist rival to Isis which shares many of its aspirations for a fundamentalist caliphate.

The decision by the two leading allies of the West to back a group in which al-Nusra plays a leading role has alarmed Western governments and is at odds with the US, which is firmly opposed to arming and funding jihadist extremists in Syria’s long-running civil war.

It threatens to trump Washington’s own attempt to train pro-Western opposition fighters, announced by President Barack Obama a year ago but finally launched only last week. The number of fighters involved is small and, crucially, the State Department insists that they would take the field against Isis and not against the regime.

The new joint approach follows an agreement reached in early March when Turkey’s President Recep Tayyip Erdogan visited the recently crowned Saudi King Salman in Riyadh, diplomats have told The Independent.

Relations had been fraught between the Turkish president and the late King Abdullah, primarily because of Turkey’s support for the Muslim Brotherhood, which the Saudi monarchy considers a threat. But Mr Erdogan stressed to Saudi officials that the lack of Western action in Syria, especially the failure to impose a “no-fly zone”, meant that regional powers now needed to come together and take the lead to help the opposition.

The Army of Conquest – which also numbers the extremist groups Ahrar al-Sham and Jund al-Aqsa among its seven members – has a command centre in Idlib, northern Syria. Turkish officials admit giving logistical and intelligence support to the command headquarters. Although they deny giving direct help to al-Nusra, they acknowledge that the group would be beneficiaries.

They also acknowledge links with Ahrar al-Sham, which is held to be extremist by the US, but has fought against Isis, as has al-Nusra in some parts of Syria. Turkish officials claim that bolstering Ahrar al-Sham will weaken the influence of al-Nusra.

Material support – arms and money – have been coming from the Saudis, say rebels and officials, with the Turks facilitating its passage. The border villages of Guvecci, Kuyubasi, Hacipasa, Besaslan, Kusakli and Bukulmez are the favoured routes, according to rebel sources.

The joint approach by Turkey and Saudi Arabia graphically illustrates how the interests of the Sunni regional powers are diverging from those of the US in Syria. Washington firmly opposes arming and funding jihadist extremists in Syria’s civil war. It conducted air strikes against al-Nusra positions in Aleppo – claiming the group was plotting terrorist attacks on the West – on the first day of the current bombing campaign against Isis.

There have been complaints from the Saudis that the US, needing the support of Shia Iran against Isis in Iraq, and hopeful of an accord over Iran’s nuclear programme, is becoming less interested in the removal of Tehran’s client regime in Damascus.

Further evidence of dissatisfaction over the US approach among Sunni states came yesterday with the news that King Salman has withdrawn from a summit with Barack Obama at the White House on the Iran nuclear talks this week: he will be represented instead by Crown Prince Mohammed bin Nayef. Of the six heads of Gulf States invited, only the emirs of Qatar and Kuwait are now due to attend.

Over Syria, the view of Sunni powers is that US action is too little, too late. It has been almost a year since Mr Obama first announced the $500m programme for the training of opposition fighters.

US officials maintained that the long run-up has been largely due to the strenuous vetting procedure for recruits. Several CIA organised “moderate” militias in the past had failed to stand up to the hardline groups and retreated, often abandoning their arms. One of the most notable and, for Washington, embarrassing, instances of this came last year when the Harakat al-Hazm gave up its bases and US funded advanced weaponry to al-Nusra. There have also widespread allegations of human rights abuses by the Western backed groups from local people.

So far, 400 recruits have been cleared by the Americans to receive light arms training in the current programme. The 90 who will start in training camps in Turkey, Jordan and Saudi Arabia are not expected to be combat ready for several months and the Pentagon estimates that it will take three years before a full force of 15,000 can be deployed.

A key sign of rapprochement between Turkey and Saudi Arabia has been over the Muslim Brotherhood. The Saudis welcomed the coup against Mohamed Morsi’s government in Egypt, but the group has been staunchly supported by Turkey since Mr Erdogan came to power. Now, say diplomats and officials, Saudi Arabia has accepted a continued role for the Brotherhood in the Syrian opposition.

Rebel fighters in Syria claim that after Western-sponsored groups lost ground to al-Nusra last year, Washington began to cut off funding for most of the supposedly moderate groups. Harakat al-Hazm, originally the most favoured of these, had its cash funding halved; the rebel Farouq Brigade had all funds cut off.

Abdulatif al-Sabbagh, an officer with Ahrar al-Sham, said: “The Americans backed people who said they were revolutionaries, but these people were corrupt and incompetent... Jaish al-Fatah is successful is because we all fight together. But we are all against Daesh [Isis] just as we are against Bashar. The Americans are bombing Daesh but doing nothing against the regime, that’s why we have got together to fight them.”

Jaish al-Fatah has made recent inroads into regime held territory, capturing Idlib and other towns and villages. Al-Nusra provided over 3,000 fighters for the operation which has put the rebels in a position to launch an offensive against Latakia on the coastal strip.