The Swedish Committee for Afghanistan (SCA), a health and education charity, said the raid on its clinic in the Tangi Saidan area of the province on Wednesday night appeared to have been carried out by members of the Afghan National Army.
Two patients and one staff member were killed in the attack in the central Wardak province, it said in a statement.
However, Afghan officials gave conflicting accounts of the raid on Thursday, saying it had not been carried out near a clinic and that the casualties had been insurgents rather than patients or staff.
A Ministry of Defence official could not confirm the information and told the AFP news agency they were looking into the report.
Wardak provincial governor Hayatullah Hayat told AFP that the area was under Taliban control, making information difficult to verify, and said the raid may have been carried out by police instead of the army.
“There was an operation by the Afghan forces, possibly police, in the area which targeted a group of enemy fighters, but it was not close to any health facility,” he said.
Four insurgents were killed, he said.
Wardak, south-west of the capital Kabul, was the scene of some of the most violent battles between Nato forces and the Taliban.
SCA, which runs health, education and other development programmes in almost half of Afghanistan's 34 provinces, strongly condemned what it said happened.
“This attack constitutes a gross violation of humanitarian principles and the Geneva Convention that all actors of a conflict have to respect,” Jörgen Holmström, the charity's country director said in the statement.
“We will further investigate this violation and let those responsible be held accountable.”
Jörgen Holmström. Photo: Malin Hoelstad/Svenska Afghanistankommittén
The attack came as the International Red Cross said on Thursday that it had suspended its activities in Ghazni province after five of its local staff there were taken hostage by what it described as a “local armed group”.
In a statement the charity said it was working to get the team released.
“ICRC's activities are currently suspended in Ghazni province. Security conditions are being reviewed in other ICRC offices, but activities are presently ongoing,” the statement said.