The investigation is the first objective look at the rating system the military has used for the past five years to judge the effectiveness of Afghan troops. Its findings seem to contradict upbeat assessments recently provided by senior military commanders overseeing the war.
The capability of Afghan forces is considered the single biggest indicator of whether the war is going well and is seen as the linchpin in the U.S. strategy since the war began more than eight years ago.
Lawmakers are likely to use the latest findings to question President Barack Obama's handling of the war. Democrats say they are frustrated that Mr. Obama is sending more U.S. troops into combat without assurances that Afghan forces are close behind.
"I think the worst nightmare for the Taliban is an Afghan army in charge," said Sen. Carl Levin, a Michigan Democrat who chairs the Armed Services Committee.
The U.S. has spent $27 billion on the effort - about half of the money it has poured into rebuilding Afghanistan. But the program has been hobbled by a lack of trainers, available Afghans and spikes in violence.
"The bottom line to this is that the system ... is flawed, it's unreliable and it's inconsistent," said Arnold Fields, who led the study as the special inspector general for Afghanistan reconstruction.
Two weeks before he was, Gen. Stanley McChrystal told reporters that "their growth is on track" and "we're ahead of the plan." But the report found that the system used to judge that success was deeply flawed. In some cases, units with the same rating would have different abilities. Also, highly rated units often regressed as soon as U.S. mentors withdrew.
In one stark example, a police district in the northern Afghan province of Baghlan was given the top rating by NATO officials in August 2008. The "CM1" designation meant the police were independently capable of conducting operations. But when investigators asked to visit the district in February, they were told the district wasn't secure and was overrun with insurgents.
One official told investigators that the police force had "withered away to the point that it barely functions."
Levin said the U.S. should delay major operations planned in the southern town of Kandahar until more Afghan troops can deploy to the fight. He called it "totally unacceptable" that there are only about 5,300 Afghan forces in Kandahar and 6,900 coalition troops being led by the U.S.
Fields said that the NATO headquarters in Afghanistan was briefed on his findings in March. Officials agreed in April to change the rating system.
In a written response to the report, NATO says it has made significant progress in both training Afghan forces and measuring their effectiveness in recent months.
Lt. Gen. Bill Caldwell, who heads the training mission in Afghanistan, said that NATO has suffered a severe shortage in trainers with some facilities on the verge of shutting down.
"Building an enduring and self-sustaining force remains a distinct challenge and attainment of the growth objectives is not assured," Caldwell wrote in a letter to investigators.
Meanwhile, Gen. David Petraeus, Mr. Obama's nomination to replace McChrystal, will try to convince a war-weary Congress on Tuesday that he is the man to turn the war in Afghanistan around and mend the military's tattered relations with civilian leaders.
Petraeus is expected to continue McChrystal's strategy in Afghanistan in large part because it is based on Petraeus' own ideas about beating an insurgency. That plan calls for more troops to bolster security while limiting the use of firepower in order to win the support of the local population.