His report, provided to The New York Times ahead of its public release, acknowledged that the aid agency was simply following a policy set by senior officials in the Obama administration, and that direct aid payments to the Afghan government would probably continue no matter what problems were found. His chief recommendation was that the agency apply more pressure on Afghan ministries to clean up their operations.

The agency, which has grown accustomed to harsh reports on its work in Afghanistan from the inspector general, characterized the latest report as one with lots of smoke but no fire. The agency said that despite all the warnings about risks, the report outlined no specific instances of fraud.

“As this audit does not examine the implementation of U.S.A.I.D. direct assistance programs, we do not believe this report has any basis on which to question whether the identified vulnerabilities have been addressed prior to funds being made available,” Donald L. Sampler Jr., the assistant to the administrator for Afghanistan and Pakistan at the agency, wrote in a letter responding to the report.

The agency also said it had taken steps to forestall fraud and would continue to do so. As an example, it cited the routing of money to each ministry’s separate account at the Afghan central bank. With the American aid funds isolated from each ministry’s general account, American officials can keep closer tabs on how the money is spent.

American officials have earmarked $896 million in assistance to date that they want to deliver directly to Afghan ministries. But because of the waste and corruption issues, they have disbursed only $201.7 million of that.

“We didn’t say, ‘We’ll give you 50 percent, come hell or high water,’ ” said S. Ken Yamashita, a U.S.A.I.D. veteran who coordinates aid spending at the American Embassy in Kabul. “We never said, ‘We will give you 50 percent even if you don’t have the right systems in place.’ We said we will work towards that, in a way that is reasonable.”

American officials are displeased with the release of the inspector general’s report, saying it is likely to infuriate the Afghan officials who allowed the auditors from the two auditing firms, KPMG and Ernst & Young, to examine their operations.