The United States and Gulf countries have been secretly backing efforts by opposition rebels to destroy al-Qaeda's most extreme wing in Syria, diplomats and rebels involved in the plan have told The Telegraph.

As Western leaders publicly push the Syrian regime and the opposition to the Geneva II peace conference that begins Wednesday Washington has also been quietly supporting moves by Saudi Arabia and Qatar to give weapons and cash to rebel groups to fight al-Qaeda's Islamic State of Iraq and al-Shams (ISIS) in Syria.

One source said the US was itself handing out millions of dollars to rebel groups best equipped to take on the extremists while another confirmed America was providing non-lethal aid.

The development marks a new phase in the conflict, with international backers working directly with rebel commanders to target al-Qaeda cells, who are seen as a major threat by Western intelligence agencies.

"Everyone is offering us funding to fight them," said one commander in a rebel group affiliated to the Western-backed Supreme Military Council. "We used to have no weapons with which to fight the regime, but now the stocks are full."

In the past year ISIS has "hijacked" the Syrian revolt. Made up partly of foreign jihadists, it has sought to impose a medieval style Islamic caliphate run under a strict interpretation of Sharia law in rebel-held areas. They assassinated rival rebel commanders who they feared might be conspiring against them, or whose power they perceived as a threat.

The final affront, in rebel eyes, came in December when ISIS tortured and killed Abu Rayyan, a popular doctor and commander in a rebel brigade.

The subsequent battle against ISIS, which began a fortnight ago and has already claimed more than 1000 lives, is being touted by local commanders as a spontaneous reaction to the spate of assassinations of comrades.

However, the Telegraph can reveal that in late December, a delegation including US and Saudi officials met in Turkey with senior rebel leaders.

According to two sources – one whose brother was at the meeting: "They talked about the fighting with ISIS, and the Americans encouraged the commanders to attack."

The Syrian Revolutionary Front, whose main commander, Jamal Maarouf, is allied to Saudi Arabia, and the Army of Islam, a new coalition of the moderate rebels sponsored by Qatar, have continued to liaise with the CIA and Saudi and Qatari intelligence, others close to meetings said.

These groups received a boost in arms supplies. According to a source who facilitates governments' lethal and non-lethal aid to Western-friendly groups: "Qatar sent arms first. Saudi Arabia didn't want to be out done, so one week before the attack on ISIS, they gave 80 tons of weaponry, including heavy machine guns".

A resident living close to bases for the Army of Islam and the Syrian Revolutionary Front in Syria's Idlib province said he had seen 15 trucks "filled with weapons going to the bases".

Washington did not directly give arms, he said, but backed Saudi Arabia in its funding of the groups. The United States has, however, also been giving $2 million in cash every month as an unofficial hand out, splitting that amount between western friendly rebel groups, the source added.

Senior commanders in both groups confirmed they had received some funds, but refused to say whether it was specifically for the purpose of attacking ISIS. They are wary of being compared to the so-called "Sunni Awakening" of 2006 in Iraq, when the US military encouraged former insurgents to rebel against their al-Qaeda allies, as many Islamist groups in Syria consider the term offensive.

Nonetheless, the recent fighting marks a dramatic change in the pace of battle, after months of stalemate in the fight against Mr Assad.

On the same day earlier this month, rebel groups, confident and well armed, launched coordinated attacks against ISIS at militarily strategic points across three different provinces in the north of the country, as well as in the central city of Hama. ISIS was also at the same time engaged in fighting across the border in Iraq's western Anbar province, where its forces tried to capture the cities of Fallujah and Ramadi.

Muhannad Issa, a rebel commander who led an assault against ISIS in the Syrian town of Salqeen, in Idlib province, said: "All the commanders united for a meeting and we agreed they had to be finished. We gave them six hours to surrender after they took one of our bases. When the ultimatum expired, we cleaned them out. In one hour we pushed them from four of their strongholds."

One activist in Salqeen, who watched local members of ISIS coming under attack, said: "Jamal Maarouf's group attacked with full force. The ISIS guys were besieged. Jamal Maarouf was screaming over the radio, 'Give up or we are coming to kill you, just as we kill the Syrian regime.' There was an Australian jihadist there, and he was trembling."

In recent days al-Qaeda's retreat has slowed. The group has retaken the Syrian city of Raqqa – its main stronghold until now – and several towns on the outskirts of Aleppo. It is also surviving, in smaller numbers, in the city of Saraqeb in Idlib province.

Nevertheless it is hoped that the inroads made against ISIS will improve support for the Syrian opposition on the ground, thereby boosting their credibility at Geneva.

In answer to suggestions that the US and Saudis are helping the rebels against the al Qaeda linked extremists a Western diplomat told the Telegraph: "Coordination is continuing with the main international supporters of the armed groups. ISIS has fought back but the momentum of the other groups is continuing and that is a good springboard for the Geneva conference".