Taliban militants will again guarantee safe passage to Red Cross staff across Afghanistan after settling a dispute that forced the medical aid agency to halt most work.

The leading humanitarian charity cut almost all its aid for Afghans after the militants withdrew protection, leaving staff and buildings open to attack.

The insurgent group had denounced the charity for allegedly failing to ensure its own militant prisoners were not mistreated or neglected in government jails.

Red Cross officials met Taliban envoys for two days of secret talks in the Qatar capital of Doha, where the insurgent movement maintains its diplomatic office.

A Taliban statement released afterwards said its fighters should “grant access to activities of the International Committee of the Red Cross and provide security for the personnel and equipment of this organisation”.

Neither side would comment on the prisoner issue, but the insurgent statement said the Red Cross had “vowed to take effective steps to address the concerns of [the Taliban]”.

“ We welcome the acknowledgement of our humanitarian principles and the renewal of our security guarantees in Afghanistan” said Juan-Pedro Schaerer, head of the Afghanistan delegation of the International Committee of the Red Cross.

The dispute two months ago had threatened to stop the work of the Red Cross, which employs 1,000 staff in the country and has worked for 30 years to ease the plight of those caught in its wars.

The group runs medical and rehabilitation centres for the wounded and has cultivated a reputation for impartiality. It makes prison visits to ensure detainees are being treated well and repatriates bodies to all factions after clashes. In 2010 it was disclosed the group had also given first aid training to Taliban fighters.

The Taliban threat came amid growing concern about attacks on health workers in Afghanistan where doctors, nurses and medics are facing intimidation, kidnap and violence from both insurgents and government forces.

“ An alarming number of health personnel have been attacked,” one international assessment warned earlier this year.

“ Health personnel are constantly being harassed, detained, kidnapped, or the worst happens and they get killed.”