Kate Stegeman, the group's communications manager, said some staff are working in other health facilities in the city, where troops have been battling Taliban insurgents.
"All critical patients have been referred to other health facilities and no MSF staff are working in our hospital," she said, using the French acronym for the organization.
"Some of our medical staff have gone to work in two hospitals where some of the wounded have been taken," she said, AP reported.
Investigations are continuing into the bombing of the hospital on Saturday, which killed at least 19 people, including 12 MSF staffers.
The group blames a US airstrike. Afghan officials claimed helicopter gunships returned fire from Taliban fighters who were hiding in the facility. Taliban has denied the allegations.
Stegeman said there were no insurgents in the facility at the time of the bombing.
President Ashraf Ghani has said a joint investigation is underway with US Forces. President Barack Obama said that he expected a full accounting of the circumstances surrounding the bombing.
The Taliban seized Kunduz last Monday but have since withdrawn from much of the city in the face of a government counterattack. Sporadic battles continue as troops attempt to clear remaining pockets of militants.
The Taliban's brief seizure of Kunduz marked the insurgent group's biggest foray into a major urban area since the 2001 US-led invasion ended their rule.
Afghan forces have been struggling to combat the Taliban since the US and NATO shifted to a support and training role at the end of last year, officially ending their combat mission in the war-torn country.