One of the US F-15 pilots, whose name has not been released but has been referred to as Dude 15, told Nato investigators later that he "had an uneasy feeling about everything".
"Both of us could tell the ground commander was really pushing to go kinetic," he said, using a military slang term for the release of bombs on a target.
Reports now say that the German commander on the ground withheld vital information from the pilots of the US jets before they dropped their bombs.
Der Spiegel obtained a secret Nato report on the incident, saying that Germany's army knewat the time of the bombing at least one of the drivers of the hijacked tankers was still alive and at the scene.
When questioned, pilots were told all individuals on the ground were "insurgents".
The classified report also stated that new Nato rules of engagement to limit civilian casualties were ignored by the German commanders.
Just four days before the deadly bombing, General Stanley McChrystal, the senior US and Nato commander in Afghanistan, sent an assessment to Robert Gates, the US defence secretary, saying that "we run the risk of strategic defeat by pursuing tactical wins that cause civilian casualties or unnecessary collateral damage".
"The insurgents cannot defeat us militarily but we can defeat ourselves."
"I lost six men from my family ... we have nothing left but our memories. We cry for them and the children cry for food"
Bibi Sharifa, villager from Omarkhail in Kunduz, Afghanistan
"A revised Tactical Directive ... was issued to all troops in theatre on 1 July 2009, which clearly described how and when lethal force should be used."
Nevertheless, his tactical directive(pdf) appears to have been ignored. Al Jazeera revisited the scene of the attack to find villagers still traumatised by the attack.
"The [Kunduz bombing] was dead against a new directive that had just been issued only a matter of days before, where civilian life is the prominent thing.
"The main point of the new strategy is to protect civilians, to make sure those casualty numbers go down", Al Jazeera's correspondent David Chater said.
But Bibi Sharifa, a resident of Omarkhail, told Al Jazeera she was still suffering since the loss of six family members.
"Three of them were my sons," she said. "I have seven grandchildren, we are in a desperate situation. We have nothing left but our memories. We cry for them and the children cry for food."
Another resident, Abdul Hanan, said "instead of bombing, they should have sent 10 or 15 foot soldiers. The villagers would have run away from the tankers.
"There was no need to do it. Why did they do this to us?"
The Afghan government's own preliminary investigation into the bombing found at least 30 civilianshad been killed.
And Chater reports that though a record number of civilians were killed in Afghanistan last year, "the bulk [were killed] by the Taliban".
"The numbers are going down of those killed by the Nato forces and the American forces, but this is an essential part of their counterinsurgency operation."
The incident has also continued to have an impact on politicsin Berlin, with Germany's army chiefand labour ministerstepping down.
Hamid Karzai, Afghanistan's president, is due to arrive in Germany for the annual Munich Security Conference on Friday while Nato leaders wrap-up a meeting on their Afghan operations in Turkey.
In the coming months, both Angela Merkel, the German chancellor, and the defence secretary are expected to testify to a parliamentary investigative committee on the political response to the bombing.
Nevertheless, General McChrystal gave one of his most upbeat assessments on the country's security.
Speaking at the Nato meeting in Istanbul on Thursday, the general contradicted warnings from other US officials, who have said Taliban attacks are becoming increasingly dangerous and destabilising.
"I believe the situation in Afghanistan is serious. I do not say now that I think it's deteriorating. I think and I said that last summer, and I believed that that was correct. I feel differently now," McChrystal said.
About 4,500 of an additional 30,000 US troops ordered in by Barack Obama, the US president, are now deployed in Afghanistan.