Hamid Karzai, the Afghan president, said: "Freedom of the press is respected and allowed and guaranteed by Afghan law. But promotion of terrorism in the name of the freedom of the press is a violation of the press and freedom of the press.
"This government is a democratic, institutionalised government ... but the story that Al Jazeera produced from Kunduz is something we must pay attention to."
Campaigning for Afghanistan's presidential elections started on Tuesday, with the growing strength of the Taliban being a central issue.
David Chater, who filed the report for Al Jazeera, said: "Intelligence forces ... accuse us of producing something that is unbalanced, with no government representative.
"That is clearly untrue. We interviewed at the same time the commander of the German forces in Kunduz, and he put his point across very clearly. That was a balanced report.
"They also accuse us of shooting essentially what is fake material, staged action from the Taliban. Qais Azimy and myself know the difference between fake footage and real footage. We did not."
Azimy was detained after being advised to come to the intelligence headquarters for an interview, while Shah was picked up from Al Jazeera's bureau by two officers.