MSF released a statement saying they had been informed of the "intrusion" of the site by a US tank, with members of a joint US-NATO-Afghan team investigating the attack.
"Their unannounced and forced entry damaged property, destroyed potential evidence and caused stress and fear," MSF said.
MSF officials expressed their anger at the "forced entry", accusing investigators of violating an agreement that the charity "would be given notice before each step of the procedure involving the organization's personnel and assets."
US Reportedly Knew Site Was a Hospital
The news of the US and NATO-led team of investigators entering the site comes amid reports that US forces operating in the area at the time of the attack knew the facility was a hospital.
According to a report by the Associated Press, an unnamed former intelligence officer said US officials were gathering intelligence on the hospital in the days leading up to the attack, over suspicions a Pakistani operative was using the site as a base.
White House spokesperson Josh Earnest, said on Thursday that he was "not aware" of the media reports and declined to comment on the motivation of the attack and who ordered the strike.
MSF has led a chorus of international condemnation of the US following the attack, which it labeled an "attack on the Geneva Conventions" and a potential war crime.
The charity says that US, coalition and Afghan officials had been thoroughly informed that the site was a hospital and have not been offered an explanation.
"We have received apologies and condolences, but this is not enough. We are still in the dark about why a well-known hospital full of patients and medical staff was repeatedly bombarded for more than an hour," MSF International President Dr. Joanne Liu said. "We need to understand what happened and why."
MSF has repeatedly said that the US and NATO forces can't be trusted to carry out a full and independent investigation into the incident and has set up on online petition calling on Obama to allow the Swiss-based International Humanitarian Fact-Finding Commission (IHFFC) to carry out an investigation into the attack.
Fears of War Crimes
The attack has also seen US forces accused of committing war crimes as a result of the bombing.
Legal experts have suggested that if it can be proven that the US knew the site was a hospital, then it could amount to war crimes.
Alternatively, if there is no evidence to suggest that Taliban fighters were using the hospital as a base — which has been rejected by MSF officials — then it is thought that the attack would also be classified as a war crime.
Thirdly, if US forces were certain that Taliban operatives were using the MSF medical center as a base, then they would have been obliged to inform the hospital of an imminent attack, with a failure to do so seen as a violation of war crimes.
MSF officials have confirmed that they were never notified that the hospital would be bombed and dismissed suggestions that the hospital was a secret base for insurgents. "Not a single member of our staff reported any fighting inside the MSF hospital compound prior to the US airstrike," according to MSF General Director Christopher Stokes.
While officials in Washington are remaining tight lipped over the events leading up to the attack, speculation grows as to whether war crimes were in fact committed.
However, the US' failure to allow independent investigators to assess the circumstances of the attack, as well as media reports suggesting officials changed their story four times in the days following the fatal bombing have led to calls that the recent intrusion into the site is part of a cover-up.