An internal State Department cable recounts new details about how Afghan President Hamad Karzai allegedly intervened on behalf of politically connected drug traffickers, prompting the U.S. government to file a formal diplomatic protest and Karzai’s own chief of staff to say he was “ashamed” of his president’s actions.

But the protest, known as a demarche, was never made public and the Aug. 9, 2009 cable detailing the U.S. government’s complaints was classified as secret by the U.S. Embassy in Kabul. The result was to downplay the depth of U.S. concerns about alleged corruption inside Karzai’s government during a period that the Obama administration was ramping up U.S. aid and troop levels in Afghanistan.

The cable, posted last night on the WikiLeaks website, shows again that at least some of the documents being disclosed by the organization are not simply diplomatic gossip, as some administration officials and news commentators have suggested. As with a January 2010 cable that appears to confirm direct U.S. involvement in a bombing raid that reportedly killed 41 civilians in Yemen, the Afghan cable sheds new light on a politically touchy subject that administration officials have preferred not to talk openly about.

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The newly revealed cable, written by U.S. Ambassador Karl Eikenberry and addressed to Secretary of State Hillary Clinton and other senior officials in Washington, reported that on July 29, 2009, Deputy Ambassador Frances Ricciardone and State Department Legal Adviser Harold Koh had formally demarched Afghanistan’s Attorney General Mohammed Ishaq Aloko.

The protest was over two issues: the Karzai government’s release of detainees, including a large number transferred from Guantanamo, and its interventions on behalf of convicted “narco-traffickers.” In April of last year, the cable recounts, Karzai pardoned five border policemen known as the “Zahir Five.” The officers had been tried, convicted and sentenced by a U.S.-funded Afghan Central Narcotics Tribunal after they had been caught with 124 kilograms of heroin in their border police vehicle. But Karzai pardoned all five of the convicted traffickers on the grounds that they were “distantly related to two individuals who had been martyred during the civil war.”

In another case, the Eikenberry’s cable states, Karzai “tampered” with the narcotics case against Haji Amanullah, “whose father is a wealthy businessman and one of his supporters." After Afghan narcotics prosecutors developed a drug case against him, Karzai “without any constitutional authority” ordered the police to conduct a second investigation against him, resulting in the conclusion that he had been “framed.”

In perhaps the most surprising passage in the cable, it recounts how Karzai’s own chief of staff, Mohammed Omar Daudzai, had told deputy ambassador Riccardone that “he was ashamed of the president for his interference in this case and the case of the Zahir Five.”

Although U.S. frustrations over Karzai’s actions were publicly reported at the time, the fact that the State Department went so far as to file a formal demarche was never publicly disclosed. Nor were U.S. concerns about the second reason for the demarche: that a detainee committee headed by Aloko was releasing large numbers of prisoners transferred from U.S. custody to an Afghan National Detention Facility despite an Afghan government commitment that the detainees would be criminally prosecuted in Afghan courts.

According to the cable, the Afghans had released 150 detainees without any trial since 2007, including 29 who had previously been at Guantanamo. (Although the cable doesn’t mention it, at least two former Guantanamo detainees transferred to Afghan custody in December, 2007, Abdul Rauf Khadim and Mullah Abdullah Zakir, have since reemerged as leaders of the Taliban.

U.S. concerns about Karzai’s and Aloko’s interventions in the Afghan judicial system have escalated since last year’s demarche. This year, U.S. officials were privately furious when Karzai intervened to free the chief of staff of his national security council, Mohammed Zia Salehi, after he was arrested on corruption charges. And the cable is not the only one in the WikiLeaks cache that has put the spotlight on allegations of corruption inside Karzai’s government.

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Another WikiLeaks cable, first reported Sunday by The New York Times, reported that Afghanistan’s Vice President Ahmed Zia Massoud had been found to have been carrying $52 million from Kabul to a Persian Gulf state.

A spokesman for the Afghan Embassy in Washington did not immediately respond to a request for comment, but Karzai’s press secretary dismissed the revelations in the WikiLeaks cables saying, “it won’t have a noticeable effect on our broader strategic relationship.”

Asked about the Eikenberry’s cable and why it was kept classified, Caitlin Hayden, spokeswoman for the U.S. Embassy in Kabul, responded today: “The Embassy cannot comment on materials, including classified documents, which may have been leaked.”