The United States and Turkey have signed a deal to train and equip Syrian rebel forces, despite concerns that very few moderate rebels remain.

“Turkey and the United States signed a document a short time ago on the train-and-equip [programme],” Turkish Foreign Minister Mevlut Cavusoglu told reporters on Thursday.

A US embassy spokesman confirmed the deal had been signed by officials from both countries in Ankara.

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The announcement puts an end to months of difficult negotiations between the NATO allies on how to train Syrian rebel forces and which enemy they should focus on.

Turkey, a vocal critic of Syrian President Bashar al-Assad, wants moderate rebels factions to be trained to battle both the regime in Damascus, as well as the Islamic State insurgents who have seized large chunks of territory in Iraq and Syria right up to the Turkish border.

Washington, whose aircraft target Islamic State positions in Syria, wants to train the rebel forces as part of its fight against the terrorist organisation.

The goal is to train more than 5,000 Syrians in the first year of the programme.

But this plan could backfire, as many Syrian rebels have reportedly declared allegiance to the Islamic State.

At the end of last year, Lebanese media reported that the Free Syrian Army, one of the largest rebel groups, had begun cooperating with terrorist groups along the Syrian-Lebanese border.

“We are collaborating with the Islamic State and the Nusra Front by attacking the Syrian Army’s gatherings in … Qalamoun,” said Bassel Idriss, the commander of an FSA-aligned rebel brigade.

“We have reached a point where we have to collaborate with anyone against unfairness and injustice,” another FSA commander, Abu Khaled, told local media.

—with AAP.