A US tank has forced its way into the shell of the Afghanistan hospital destroyed in an airstrike 11 days ago, prompting warnings that the US military may have destroyed evidence in a potential war crimes investigation.

The 3 October attack on the Médécins sans Frontières (MSF) hospital in Kunduz killed 10 patients and 12 staff members of the group.

In a statement on Thursday, the medical charity, also known as Doctors Without Borders, said they were informed after Thursday’s “intrusion” that the tank was carrying investigators from a US-Nato-Afghan team which is investigating the attack.

“Their unannounced and forced entry damaged property, destroyed potential evidence and caused stress and fear,” MSF said.

The Pentagon did not immediately respond to a request for comment on the reported intrusion, which came as new evidence emerged that US forces operating in the area at the time of the attack knew that the facility was a hospital.

US special operations analysts were gathering intelligence on the hospital days before the attack, because they believed a Pakistani operative was using it as his base, according to areport by the Associated Press citing an unnamed former intelligence official.

The analysts had mapped the area and drawn a circle around the hospital, the official was quoted as saying. The Pakistani man, described both as a Taliban suspect and as a worker for the Pakistani Inter-Service Intelligence directorate, was killed in the attack, the official told the AP.

Of the nearly 200 patients and staff inside the hospital at the time of the attack, more than three dozen were wounded, said MSF, which has called the attack a violation of the Geneva Conventions and a war crime. The group has said some patients burned to death in their beds.

Several investigations of the attack are considering whether the separate American teams involved – special operations analysts, intelligence community officers, the military command that ordered the strike – knew the facility was a hospital, whether they gave warning of a strike and what was happening on the ground at the time.

It is unclear whether the analysts’ knowledge that the facility was a hospital was shared by the command that launched the attack. MSF said GPS coordinates identifying the hospital had been shared with US, coalition and Afghan military officers and civilian officials “as recently as Tuesday 29 September”.

Michael Newton, a West Point graduate and an expert on conduct of hostilities issues at Vanderbilt Law School, listed questions a Defense Department investigation would seek to answer.

“There’s somebody in some part of the force that knows that’s a prohibited target,” Newton said. “The question then is, what are the fire control measures over that place?

“If they were followed, were they adequate? If they weren’t followed, why weren’t they followed? And underneath that, there’s two things. Either, one – they were misapplied. Or, two, there was an exception.”

An example of an exception would be a case of self-defense, Newton said.

The Pentagon originally said the hospital was struck in the course of a firefight involving US troops. General John Campbell, the top US officer in Afghanistan, later said the strike on the hospital was a mistake.

The Pentagon declined further comment on Thursday, citing ongoing investigations.

The Defense Department, Nato and the Afghan government are conducting parallel investigations of the attack, while MSF has called for an inquiry by the International Humanitarian Fact-Finding Commission, or IHFFC, a never-before-used investigative commission under the Geneva conventions.

“It is impossible to expect the parties involved in the conflict to carry out independent and impartial investigations of acts in which they themselves are implicated,” said MSF in the statement on Thursday. “The preservation of health facilities as neutral, protected spaces depends on [an independent investigation].”

US and Afghan consent is needed for the IHFFC investigation to proceed. MSF launched an online petition on Thursday calling on President Barack Obama to consent.

The White House spokesman, Josh Earnest, said on Thursday that he was “not aware” of the Associated Press report. He declined comment on who gave the order for the strike on the hospital or the motivation for the attack.

“All of those are questions that will be considered by the ongoing Defense Department investigation,” Earnest said. “The president’s expectation is that he will see a full accounting of these facts in context.”

Newton said the Pentagon investigation would be drawing on a wealth of evidence.

“There’s a limited time frame here, it’s a discrete incident, there would be radio logs or at least handwritten notes of radio traffic – I think they’ll absolutely get every relevant fact,” he said.

Newton said the White House silence on the issue of whether the attack could constitute a war crime was appropriate.

“People say, ‘Why won’t the president just call it a war crime, why won’t the secretary of defense just call it a war crime, let’s be honest, that’s what it was’,” said Newton. “The answer is, because in the US military it is a separate offense – unlawful command influence – if higher-level political officials or military officials prejudge a case and start talking about it in public.”

“What actually happened on the ground? That’s the unanswered question.”