Doctors Without Borders said the "intrusion" Thursday was by a joint US-NATO-Afghan team investigating the Oct. 3 bombing.
The group says the incident violated an agreement that they "would be given notice before each step of the procedure involving the organization's personnel and assets."
"Their unannounced and forced entry damaged property, destroyed potential evidence and caused stress and fear," it said in a statement.
The strike in Kunduz killed 10 patients and 12 staff. US President Barack Obama apologized for the bombing, which the commander of US and NATO forces in Afghanistan called a "mistake.