David Chater, Al Jazeera's correspondent in Kabul, said on Tuesday: "We still don't know what happened to both our producers, where they're being held and what the charges might be.
"The intelligence agency says that they consider the package I put together last week with material taken by Qais with the Taliban around Konduz to be unbalanced and that the scenes that were taken by Qais were actually artificially created," he said.
Chater said: "They now have ordered my to produce a full transcript of both my script and my package. We await their verdict."
Al Anstey, Al Jazeeera English's director of news, said: "We stand by the report filed by David Chater on Thursday June 11 which was produced by Qais Azimy in Kunduz province of Afghanistan.
"We were involved in the commissioning of the piece and approved all elements of the production. All stories we air on Al Jazeera English go through the toughest scrutiny and uphold the highest standards of balance and journalistic integrity.
"We would never tolerate any content being "artificially created" for AJE. Qais Azimy is a trusted member of our full time staff, and is one of the best journalists in Afghanistan," he said.
Chater said that the taxi driver who had taken Azimy to the headquarters was sent away from the building after waiting for him to return for about six hours.
"We've repeatedly tried to find out exactly what happened," he said.
"We've tried every single lever we know here ... we are in an information vacuum."
Chater said that Hamid Karzai, the Afghan president, the UN and the International Security Assistance Force (Isaf) had been contacted to see if they can provide any information on the situation, without success.
"With the election [campaigning] starting here tomorrow, it is a very sensitive time," he said.
Chater said the Afghan authorities may have been angered by a report made by Azimy showing him meeting Taliban fighters around the town of Kunduz in the north of the country, which was broadcast on Friday.
In an interview conducted by Azimy, a Taliban leader said he had hundreds of men under his control and 12 suicide bombers waiting to strike.
With campaigning for the presidential elections due to start on Tuesday, the growing strength of the Taliban insurgency is due to be a central issue.