MSF said its policy is not to accept government money for its operations in Afghanistan and elsewhere around the world.
"This policy allows us to work independently without taking sides and provide medical care to anyone who needs it. This will not change," the nonprofit said in a statement.
Last week, MSF General Director Christopher Stokes said that the all of the information about the attack released so far makes it "hard to understand" how the Pentagon maintains the bombing was some sort of "mistake."
MSF believes the attack was deliberate, and therefore a war crime. The group has repeatedly called for an independent investigation by the International Humanitarian Fact-Finding Commission.
But Washington maintains that investigations launched by the US and Afghan governments, as well as NATO, will be sufficient.
Since the attack, much of the debate has centered on whether Taliban patients in the hospital were armed, and if the group was using the building as a base of operations.
Doctors Without Borders released its own findings last week, denying that any combatant, whether the Taliban or the Afghan government's, was armed inside the compound.
The Pentagon said shortly after the attack that they intended to pay for the repairs and to make "condolence payments" to the families of civilians killed. The Pentagon also promised to pay for additional repairs after smashing the hospital with an armored vehicle.