The Swedish Committee for Afghanistan (SCA) said the raid on its clinic in the Tangi Saidan area of the province tomorrow 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, it said in a statement.
However Afghan officials gave conflicting accounts of the raid today, saying it had not been carried out near a clinic and that the casualties had been insurgents rather than patients or staff.
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.
Another senior Afghan official confirmed a raid had taken place but said it was nowhere near a clinic.
The 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," Jorgen Holmstrom, the charity's country director said in the statement.
"We will further investigate this violation and let those responsible be held accountable.
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