Kabul had hailed the transfer of Bagram prison, sometimes called the Guantanamo Bay of Afghanistan, as a victory for national sovereignty as Nato prepares to hand over security to Afghans and withdraw its combat troops by the end of 2014.
Karzai had demanded authority over the prison as a condition for signing a long-term agreement covering Afghan-US relations after the pull-out of combat troops in 2014.
But prisoners found innocent by courts were still being held and more people had been captured by American forces against the provisions of the agreement, a statement from the president's office said Monday.
The president condemned what he called "a serious breach of the memorandum of understanding" with the United States after the completion of a two-month timeline agreed for the full transfer of the prison.
"The president assigned the minister of defence, the attorney general, and the chief commander of Bagram prison to take all required and urgent measures to ensure a full Afghanization of the prison affairs and a complete transfer of its authority," it added.
There was no immediate comment from the US embassy in Kabul.
The US formally handed control of the prisoners to Afghan authorities on September 10, but disagreements remained over the fate of hundreds of inmates.
Under the agreement, Afghan authorities will need to advise the US of plans to release any prisoners and "consider favourably" objections if the Americans consider such inmates could engage in "terrorist activity".
In turn, the Afghans would give the US and humanitarian bodies access to detainees to monitor their treatment under international humanitarian law.
Human rights campaigners have regularly criticised the prison under US control, saying it fails to comply with international norms as some inmates are detained arbitrarily without trial or knowledge of the charges against them.
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Hamid Karzai would you like to explain honestly,sincerely,truly and completely did ever US fulfill any promise till now regarding any other countries' and their people's interests,self-reliance and sovereignty besides its own,its own people's and national's interests??????