KABUL, Afghanistan — President Hamid Karzai of Afghanistan has promised to root out corruption, but after one of his own top aides was arrested by American-supported anti-graft units recently, he fired back by investigating the investigators and apparently seeking control over their actions.

He convened a commission ultimately reporting that the anti-corruption investigators were violating the human rights of suspects they arrested. Aides to the president also complained that they violated the nation’s sovereignty because of the American role in the investigations.

The controversy set up yet another serious divide between American officials and Karzai at a time when the Obama administration has made combating corruption in the Afghan government a major policy goal. Congress is withholding $4 billion in financing to Afghanistan over a case closely related to the arrest of Karzai’s aide.

At issue are two powerful anti-corruption organizations set up in the Ministry of the Interior, initially with the president’s approval, known as the Major Crimes Task Force and the Sensitive Investigative Unit. American agencies, including the FBI and the Drug Enforcement Administration, are extensively involved in the units.

They are self-contained, with their own lawyers, investigators, judges and even detention facilities. The arrangement was meant to insulate them from interference from other government agencies.

The Karzai aide, Mohammed Zia Saleh, head of administration for Afghanistan’s National Security Council, was arrested in late July. According to a Western official with knowledge of the case, the arrest came after investigators wiretapped Saleh soliciting bribes from the New Ansari Exchange, a money exchange operation, to impede an investigation into the company’s role in exporting large amounts of cash from the country.

Congress held up the Afghan financing after The Wall Street Journal reported that some $3 billion had been transferred out of Afghanistan — a huge amount considering the country’s gross national product of only $13.5 billion, according to The Journal account. The New Ansari Exchange was involved in many of those money transfers, and the organization was raided by the American-backed investigators, who seized many of its records.

As recently as Thursday, the U.S. special inspector general for Afghanistan reconstruction, Arnold Fields, in an audit focused on corruption, said American agencies were still investigating where those money transfers were coming from.

"Corruption and/or fraud may or may not be the case," he said. "However, if there were systems in place to address corruption issues, there would be more confidence in the Afghan government, less corruption and less immediate suspicion of corruption."

In addition, Fields noted, the United States is planning to begin disbursing up to half of its planned $20 billion in aid to Afghanistan through the Afghan government and its agencies, rather than directly to contractors as it does now. That would require confidence in Afghanistan’s anticorruption efforts.

Another Western official, who spoke on the condition of anonymity because of the sensitivity of the dispute, said there was no doubt that the presidential commission’s investigation of the two anti-corruption organizations was prompted by Saleh’s arrest. Two delegations were sent to them from Karzai to complain about it, he said.

"There was a big spat," he said.

Saleh was later released on the order of the attorney general’s office.

The commission that Karzai appointed to investigate the anti-corruption agencies held a news conference Thursday to report its findings. Attorney General Mohammed Ishaq Alko and Mohammed Yassin Usmani, head of the country’s high office of oversight and anti-corruption, with other officials, insisted that their investigation was only coincidental to Saleh’s arrest.

They said they investigated conditions at the Qasaba Detention Center in Kabul, where the Major Crimes Task Force has 52 detainees on drug trafficking and corruption charges, and raised concerns about whether conditions there were humanitarian and Islamic. They also looked into the organizations’ investigative practices.

The commission members said they were presenting their findings to Karzai, who would review whether legislation was needed to better control the two organizations’ activities.

A subsequent statement from the president’s office Thursday night said concerns had been raised about whether the two organizations were in accord with Afghanistan’s Constitution, its "national sovereignty" and humanitarian principles. Karzai would issue a new decree governing the two organizations, the statement said, and until then the commission would be in charge of overseeing them.

A Western diplomat, who declined to be further identified as a matter of policy, said the investigative agencies were "basing their work on the highest standards of respect for human rights, civil liberties and the law."

American officials said they remained hopeful that Karzai would decide not to take any action to hinder the organizations.

Shutting down the anti-corruption units could be the biggest point of contention between the two countries since complaints about fraud in Karzai’s re-election last year. Caitlin Hayden, spokeswoman for the U.S. Embassy, recalled Karzai’s commitments at a conference here in July that included "pledges to undertake all necessary measures to increase transparency and tackle corruption, and to provide resources and enabling legislation for the Major Crimes Task Force."

"The president has ordered that the commission review every case that the MCTF has dealt with or made a decision on," said Waheed Omer, Karzai’s spokesman, using the acronym for the task force. "We are not saying we will dismantle the MCTF. The president wants to bring it under the existing structures of law and order."

Another senior Afghan official, speaking on the condition of anonymity because of the sensitivity of the issue, said a major concern of the president was the role of foreigners in running the Major Crimes Task Force.

"Our assessments show that the MCTF purports to be an Afghan institution, but is run by others," the official said, clearly referring to Americans. The official also claimed that wiretaps were made without judicial review, a charge that American officials deny.

Another high-ranking Afghan official maintained that Karzai’s concern was not because of Saleh’s arrest, which he accepted as part of the anti-corruption agencies’ mandate, but because he felt too much power had been concentrated in the units. The official said the president had not realized they would oversee every step of the investigative and judicial process, but thought of them as investigative entities that would hand their findings over to other existing agencies for prosecution.

Top officials of Karzai’s administration were actively involved, however, when the groups were initially established, and their roles were publicized.