The Wall Street Journal article paraphrased Gen. Stanley McChrystal as saying the Taliban has gained the upper hand. The article was titled, "Taliban Now Winning," though McChrystal was not explicitly quoted saying those words in the story.
Pentagon spokesmen called the interpretation of McChrystal's remarks "inaccurate" and "disappointing."
"That's not how we are characterizing this," spokesman Geoff Morrell said. He acknowledged that the insurgency is doing better in some parts of the country than the administration would like, but said it is not accurate to say McChrystal thinks the Taliban has the upper hand or is winning.
Morrell suggested that McChrystal's position was more accurately reflected in an interview he gave to USA Today.
"I wouldn't say we are winning or losing or stalemated," McChrystal told USA Today. The U.S. commander said in that interview that the insurgency has "momentum" which coalition forces are working to reverse.
The dispute over the course of the war comes as McChrystal prepares to present a comprehensive assessment of operations in Afghanistan -- an assessment that could eventually include requests for additional U.S. troops.
Top brass are insisting that despite the sharp rise in casualties in July and an expectation of more bloody months ahead the war is not taking a turn for the worse.
National Security Adviser Jim Jones, who left the door open to more troops, told CBS' "Face the Nation" on Sunday that the war is not at a "crisis level."
Rear Adm. Gregory Smith, communications director for NATO's International Security Assistance Force Office, also released a statement Monday to rebut the Wall Street Journal story.
"To clarify, the commander did not say the Taliban was winning, in his interview with The Wall Street Journal as suggested by the headline. He explained that International Security Assistance Forces are facing an aggressive enemy, employing complex tactics that is gaining momentum in some parts of Afghanistan," he said. "During the course of the interview he also observed that insurgents in Afghanistan face their own problems in terms of popularity, cohesiveness and ability to sustain morale and fighting capacity."