US special operations analysts knew a site in Kunduz, Afghanistan, which was hit by an airstrike that killed at least 22 people earlier this month was a hospital.
The Associated Press has learned that US special operations analysts were gathering intelligence on the facility run by medical aid group Doctors Without Borders because they suspected it was being used by a Pakistani operative to coordinate Taliban activity.
It is unclear whether commanders who unleashed an AC-130 gunship on the hospital on October 3 were aware that the site was a hospital or knew about the allegations of possible enemy activity.
The Pentagon initially said the attack was to protect US troops engaged in a firefight and has since said it was a mistake.
Doctors without Borders disputes that the hospital was being used by the Taliban for military purposes.
The special operations analysts had assembled a dossier that included maps with the hospital circled, along with indications that intelligence agencies were tracking the location of the Pakistani operative and activity reports based on overhead surveillance, according to a former intelligence official.
The intelligence suggested the hospital was being used as a Taliban command and control centre and may have housed heavy weapons.
After the attack, which came amid a battle to retake the northern Afghan city of Kunduz from the Taliban, some US analysts assessed that the strike had been justified, the former officer says.
They concluded that the Pakistani, believed to have been working for his country’s Inter-Service Intelligence directorate, had been killed.
No evidence has surfaced publicly to support those conclusions about the Pakistani’s connections or his death.
The top US officer in Afghanistan, General John Campbell, has said the strike was a mistake, but he has not explained exactly how it happened or who granted final approval.
He also told Congress he was ordering all personnel in Afghanistan to be retrained on the rules governing the circumstances under which strikes are acceptable.
The new details about the military’s suspicions that the hospital was being misused complicate an already murky picture and add to the unanswered questions about one of the worst civilian casualty incidents of the Afghan war.
They also raise the possibility of a breakdown in intelligence sharing and communication across the military chain of command.
Pentagon officials declined to comment.
The international humanitarian agency that ran the facility, Doctors without Borders, has condemned the bombing as a war crime.
The organisation says the strike killed 12 hospital staff and 10 patients, and that death toll may rise. It insists that no gunmen, weapons or ammunition were in the building.
The US and Afghan governments have launched three separate investigations.
President Barack Obama has apologised, but Doctors without Borders is calling for an international probe.