US special forces are supporting anti-Taliban militias in at least 14 areas of Afghanistan as part of a secretive programme that experts warn could fuel long-term instability in the country.

The Community Defence Initiative (CDI) is enthusiastically backed by Stanley McChrystal, the US general commanding Nato forces in Afghanistan, but details about the programme have been held back from non-US alliance members who are likely to strongly protest.

The attempt to create what one official described as "pockets of tribal resistance" to the Taliban involves US special forces embedding themselves with armed groups and even disgruntled insurgents who are then given training and support.

In return for stabilising their local area the militia helps to win development aid for their local communities, although they will not receive arms, a US official said.

Special forces will be able to access money from a US military fund to pay for the projects. The hope is that the militias supplement the Nato and Afghan forces fighting the Taliban. But the prospect of re-empowering militias after billions of international dollars were spent after the US-led invasion in 2001 to disarm illegally armed groups alarms many experts.

Senior generals in the Afghan ministries of interior and defence are also worried about what they see as a return to the failed strategies of the Soviet Union during its occupation of Afghanistan.

Thomas Ruttig, co-director of the Afghanistan Analysts Network, said the US risked losing control over groups which have in the past turned to looting shops and setting up illegal road checkpoints when they lose foreign support.

"It is not enough to talk to a few tribal elders and decide that you trust them," Ruttig said. "No matter how well-trained and culturally aware the special forces are they will never be able to get to know enough about a local area to trust the people they are dealing with."

Another controversial aspect of the programme is the involvement of Arif Noorzai, an Afghan politician from Helmand who is widely distrusted by many members of the international community.

Although many western officials want to sideline Noorzai and give oversight to the Afghan army and police, some of the CDI militias will build upon the 12,500 militiamen in 22 provinces Noorzai helped to set up this summer in the run up to the presidential elections on 20 August, an official said.

Despite the lack of any announcement about the programme, which could radically affect conditions in unstable areas across Afghanistan, it has begun in 14 areas in the south, east and west, but is expected to extend far beyond that.

Another diplomat in the south-east of the country said in the last six weeks special forces have held several meetings with elders in restive districts in Paktia, close to the Pakistani border, seeking to embed themselves with the local people.

The diplomat said: "It is not clear anything has happened yet, but the elders in the area are all seeing dollar signs and very much want to qualify for this programme."

According to some western officials, the US government will make a pot of $1.3bn (£790m) available for the programme, although the US embassy said it could not yet comment on CDI.

A US military spokesman also declined to comment saying the programme was still in its early phases and public discussion could jeopardise the lives of some of the Afghans involved.

The plan represents a significant change in tack from a scheme promoted just last year by General McChrystal's predecessor, David McKiernan. The Afghan Public Protection Force (APPF) was piloted in Wardak province and involved the rigorous vetting of recruits who were then given basic training, a uniform and came under the authority of the Afghan police.

"McChrystal was always quite dismissive about APPF," a senior Nato official in Kabul said. "It was too resource-intensive and so slow we would have lost long before it had been spread to the whole country."

He added: "He wanted to move to a much more informal model, which is far less visible and unaccountable, using Noorzai to find people through his own networks and then simply paying out cash for them to defend their areas."

The US has shared few details of its plans with its allies. The programme is controlled by a newly created special forces group that reports directly to McChrystal as head of US forces in the country, but which sits outside the authority of the International Security Assistance Force, the Nato mission in Afghanistan.