The Swedish Committee for Afghanistan (SCA) said troops entered the hospital in Shaniz, in Wardak province south of Kabul, late on Wednesday "without giving any reason or justification".
"They searched all rooms, even bathrooms, male and female wards," the SCA said in a statement on its website, quoting country director Anders Fange.
"Rooms that were locked were forcefully entered and the doors of the malnutrition ward and the ultrasound ward were broken by force to gain entry.
"Upon entering the hospital they tied up four employees and two family members of patients at the hospital. SCA staff as well as patients, even those in beds, were forced out of rooms (and) wards throughout the search," it said.
Describing the incident as unacceptable, the SCA said the military action was "a clear violation of globally recognized humanitarian principles about the sanctity of health facilities and staff in areas of conflict".
It said it also breached civil-military agreements between non-governmental organisations and the International Security Assistance Force (ISAF), which along with the US has more than 100,000 foreign troops in Afghanistan.
The incident lasted two hours, after which the troops "issued verbal orders" that any patient who might be an insurgent must be reported to coalition forces.
An ISAF spokesman said an investigation had been launched but no information would be available until it was completed.
The SCA has been operating in Afghanistan since the 1980s, working in 16 provinces mostly in the east, in education, health and disability.
News of the incident comes after a NATO air strike in the northern province of Kunduz early on Friday that officials have said killed or injured 90 people.
That incident reignited anger among ordinary Afghans about what can be heavy-handed tactics by foreign troops fighting a resurgent Taliban militia that have refined their tactics and are killing record numbers of international soliders.