Aid group Swedish Committee for Afghanistan says Nato and Afghan troops damaged its building and used it as jail

Nato forces stormed into a clinic in central Afghanistan, damaging doors, windows and medical equipment, before using it as a jail and military command centre, in violation of the Geneva conventions, according to the aid group that runs the facility.

Nato and Afghan troops were dropped off by helicopters late one October evening and headed straight to the clinic, according to the Swedish Committee for Afghanistan, which has published details of the assault on their small centre in Wardak province, a few dozen miles south-west of Kabul.

The soldiers knocked down a wall to enter the building, damaged doors, windows, examination beds and other equipment, and detained clinical staff and civilians inside. And for the next two and a half days they brought dozens, maybe hundreds of prisoners through the clinic, using it as a jail, logistics hub and for mortar fire, contravening the Geneva conventions, which protect medical centres.

"The protection of medical persons and facilities, and respect for their neutrality was one of the founding principles of international humanitarian law," said Erica Gaston, a human rights lawyer and senior programme officer at the US Institute of Peace.

"This latest incident is a serious violation … if true, it's incredible to me that they not only raided this clinic but that [Nato] command allowed them to continue occupying it for days afterwards."

The takeover of the clinic was the worst assault on the Swedish Committee's medical services since a bitter civil war over a decade ago, said the group's country director, Andreas Stefansson.

"I can't recall when we have had a clearcut occupation of a clinic for several days. We'd have to go back to the 1990s where you'd have warring groups that would kick out the medical staff and take over the whole building," he told the Guardian in Kabul.

Afghanistan is in desperate need of help to improve healthcare for its 30 million people. It is one of just three countries where polio is still endemic, one in five children die before their fifth birthday, and in southern provinces acute malnutrition among infants is near the levels expected in a famine zone.

But Stefansson said aid groups working on health issues felt their work was being seriously undermined because of regular abuse of their buildings and staff by government forces and troops from the Nato-led International Security Assistance Force (Isaf). The Swedish Committee has decades of experience in Afghanistan.

"Most NGOs who deliver healthcare in this country experience this almost on a monthly basis; that there are breaches in different provinces, where the Afghan National Army, or ISAF, or special forces basically don't show the level of respect they should for health facilities," he said, after meeting other healthcare organisations to discuss the problem. "We are getting quite fed up with it."

Among the most common problems are soldiers forcing their way into a hospital while searching for insurgents, demanding medical records, and pressuring doctors and nurses for treating suspected Taliban, sources from the health sector said.

The military and police have sometimes set up headquarters in compounds that house hospitals and clinics, or just outside, and medical facilities get caught in crossfire, or are used as cover during attacks.

Insurgents have targeted healthcare facilities with deadly assaults, including a truck bomb at a hospital in Logar province that killed dozens last summer. The Swedish Committee said that this autumn in Wardak province a suicide bomber damaged a midwifery school and dormitory they ran, and a bomb destroyed part of another clinic.

Ultimately it is Afghans in need of medical help who suffer from the intrusions as fearful civilians stay away, and it gets harder to recruit qualified staff in troubled areas. When government or Nato forces use compounds, insurgent groups are more likely to harass doctors, nurses and the centres from which they operate.

"It puts us in jeopardy because [local people] of course question the neutrality of the healthcare delivered, and it also puts us in problems with opposition groups who believe we have alternative agendas," Stefansson said.

The Swedish Committee said it had met Isaf commanders, who acknowledged the takeover breached international laws, said the use of the clinic was a mistake, and promised "actions will be taken" to avoid similar incidents.

"Isaf confirmed at the meeting that their policies are clear regarding respecting the Geneva conventions, claiming that the occupation of the clinic was unintentional," the group said in a statement.

Isaf did not respond to a request for comment on the incident.