"My best military judgment is that the situation is, in some ways, deteriorating."
He went on to say that unrest across the country was up, and it was up "not only because there are more coalition forces, it is up because the insurgency is growing".
McChrystal has previously said that the mission in Afghanistan, involving 100,000 foreign troops of which about 60,000 are American, faces failure unless the strategy changes.
"We must do things dramatically differently, even uncomfortably differently"
General Stanley McChrystal
He also believes, according to US officials, that up to 40,000 more troops and trainers are needed.
His recommendations on how to pursue the conflict have been handed to the Pentagon and the White House.
Barack Obama, the US president, is now holding discussions with policy experts and analysts and is expected to make a decision on troop deployments within the next few weeks.
McChrystal refused to comment further on how many more troops he wants, saying only that he believed "resources and goals" would be aligned in the end. But he said those fighting the war needed to be ready to do things differently.
"Whether we like it or not, we have a conventional warfare mentality," he said. "We must do things dramatically differently, even uncomfortably differently," he said, referring to the need to take risks to protect Afghan civilians.
"I discount immediately anyone who simplifies the problem or offers a solution ... or says 'this is what you have got to do' because they absolutely have no clue about the complexity of what we are dealing with."