David Chater, Al Jazeera's correspondent in the capital Kabul, who helped compile the report, said he was trying to find out more information about what was happening to his colleagues.
"We don't know what they are charged with. We don't know when they might be released. We know absolutely nothing," he said.
"Intelligence forces that are holding our two producers ... 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," he said.
"It would appear that we are suffering from the fact that we are delivering an uncomfortable and unpalatable truth in our messages.
"So that means, once again, that somebody, somewhere in Kabul and in the government is trying to shoot the messenger."
Al Anstey, Al Jazeera 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.
|Chater said the report was accused of being 'unbalanced', but interviews prove otherwise
"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.
Azimy, a senior producer for Al Jazeera English, was detained after travelling to the intelligence headquarters in the Afghan capital after being told to meet authorities for an interview.
Shah, who works for the Al Jazeera Arabic television channel, was simultaneously picked up from the network's bureau by two officers.
Hamid Karzai, the Afghan president, the UN and the International Security Assistance Force (Isaf) have been contacted to see if they can provide any information on the situation, Chater said, but without success.
Campaigning for the presidential elections started on Tuesday, with the growing strength of the Taliban insurgency being a central issue.