Doctors Without Borders said on Thursday that the U.S. broke an agreement when one of its tanks forced its way through the closed gates of the compound without prior notification.

The medical charity, also known as MSF, said they were only informed after the “intrusion” that it was by a delegation from a joint U.S.-NATO-Afghan team investigating the Oct. 3 bombing of the hospital in the northern Afghan city of Kunduz.

The incident violated an agreement with investigators that MSF "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, adding that an MSF team had arrived at the hospital earlier in the day.

The U.S. military airstrike on the MSF trauma center in Kunduz killed 10 patients and 12 staff members. Another two staffers are now presumed dead, the group said this week. The rest of the staff have been accounted for.

The report of the “intrusion” comes as the Associated Press reported Thursday that American special operations analysts were gathering intelligence on the hospital because they believed it was being used by a Pakistani operative to coordinate with Taliban activity.

These analysts had the hospital marked on a map they were using to track the location of the alleged operative, a former intelligence official with knowledge of the documents told the Associated Press. The intelligence suggested the hospital was being used as a cover for a Taliban command and control center and may have housed heavy weaponry.

After the strike was conducted, Doctors Without Borders said none of its staff was Pakistani. The medical staff has condemned the attack as a war crime and insisted that no gunmen or weapons were in the building.

What the new details suggest "is that the hospital was intentionally targeted, killing at least 22 patients and MSF staff," Meinie Nicolai, president of the operational directorate of Doctors Without Borders told the Associated Press. "This would amount to a premeditated massacre. ... Reports like this underscore how critical it is for the Obama administration to immediately give consent to an independent and impartial investigation by the International Humanitarian Fact-Finding Commission to find out how and why U.S. forces attacked our hospital."

President Obama apologized for the bombing, which the commander of U.S. and NATO forces in Afghanistan, Gen. John F. Campbell called a "mistake."

"To be clear, the decision ... was a U.S. decision made within the U.S. chain of command,” Campbell said days after initially defending the strike and intelligence. “A hospital was mistakenly struck. We would never intentionally target a protected medical facility."

The bombing happened as Afghan forces battled Taliban insurgents who had stormed Kunduz on Sept. 28 and briefly held the city of 300,000, the first provincial capital they have overrun since being forced from power in 2001.

Government troops have largely retaken the city, where authorities say life is returning to normal. Casualty figures have not yet been made public.

The seizure was a grave embarrassment for the government of President Ashraf Ghani. On Thursday, Obama said he would keep nearly 10,000 U.S. troops in Afghanistan through most of next year and 5,500 when he leaves office in 2017, throwing a lifeline to the struggling Afghan forces.

The Associated Press contributed to this report.