Medecins Sans Frontieres (MSF) has said it is "disgusted" by Afghan government statements justifying an air strike on its hospital in Kunduz, calling it an "admission of a war crime".
The charity said the statement implies US and Afghan forces decided to bomb a hospital because of claims Taliban members were inside.
The charity blames US-led Nato forces for Saturdays attack which killed at least 22 people, including MSF staff.
The US is investigating the incident.
Afghan government forces, backed by the US-led coalition, are engaged in a battle to retake the northern city of Kunduz from Taliban fighters who seized it last month.
On Saturday, the Afghan defence ministry said "armed terrorists" were using the hospital "as a position to target Afghan forces and civilians".
MSF said in a statement: "These statements imply that Afghan and US forces working together decided to raze to the ground a fully functioning hospital - with more than 180 staff and patients inside - because they claim that members of the Taliban were present.
"This amounts to an admission of a war crime. This utterly contradicts the initial attempts of the US government to minimise the attack as 'collateral damage.'"
US Defence Secretary Ashton Carter said on Sunday that a full, transparent investigation would be conducted into whether the US military could be linked to the attack.
MSF re-iterated its demand for an independent investigation by an international body.
Twelve MSF staff members and 10 patients were killed when the hospital was hit.
Dozens were injured and the hospital severely damaged by a series of air strikes lasting more than an hour from 2am local time on Saturday morning.
Death toll from bombing of @MSF hospital in Kunduz now 22: 12 MSF staff & 10 patients, including 3 children, killed in attack— MSF International (@MSF) October 4, 2015
On its Twitter feed, MSF said: "The hospital was repeatedly and precisely hit during each aerial raid, while the rest of the compound was left mostly untouched.
"Not a single member of our staff reported any fighting inside the hospital compound prior to the US air strike on Saturday morning."
Staff pulled out of Kunduz
Afghan troops are now reported to have recaptured most of Kunduz after it was seized by the Taliban.
MSF said it was pulling most of its staff out of the area but some medical staff were treating the wounded at other clinics.
"All critical patients have been referred to other health facilities and no MSF staff are working in our hospital," a spokeswoman for the charity told AFP.
MSF says the hospital was a lifeline for thousands in the city and in northern Afghanistan.
US President Barack Obama has expressed his condolences and said he would await the conclusions of an inquiry before making a definitive judgement.
The UN called the strikes "inexcusable and possibly even criminal", with Secretary General Ban Ki-moon calling for a thorough and impartial investigation.