Masoom Stanekzai told The Associated Press in an interview that Taliban insurgents and possibly Pakistani intelligence operatives were using the facility in Kunduz city as a "safe place."
The hospital was bombed by a U.S. AC-130 gunship in the early hours of Oct. 3, killing at least 22 people and injuring many more.
The main building was destroyed and the hospital has been shut down.
"That was a place they wanted to use as a safe place because everybody knows that our security forces and international security forces were very careful not to do anything with a hospital," Stanekzai said.
"But when there was on one of the walls of the hospital, there was a Taliban flag — what can you think?"
The group, also known by its French acronym MSF, has repeatedly denied the presence of Taliban fighters in the hospital compound at the time of the attack.
Kate Stegeman, MSF's communications director in Afghanistan said on Monday: "We reiterate that every staff member in Kunduz working for MSF has repeatedly reported to us that there were no armed people in the hospital at the time of the bombing."
Doctors without Borders has acknowledged that it treated wounded Taliban fighters at the Kunduz hospital, but it insists no weapons were allowed in.
Afghans who worked at the hospital have told the AP that no one was firing from within.
But Stanekzai insisted that a Taliban flag had been hoisted on the walls around the hospital compound and that the militants were using it as a base.
"I am saying the compound was being used by people who were fighting there, whether it was Taliban or ISI or whoever they were," he said, referring to Pakistan's powerful Inter-Services Intelligence agency, long accused by Kabul of supporting the Taliban.
"If the fighting was not coming from there, that kind of a mistake will never happen." Read more: