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But a few weeks ago, the U.S. stopped all transfers.

“Some 99 percent of the detainees captured before 9 March have already been transferred to Afghan authority, but we have paused the transfer of the remaining detainees until our concerns are met,” said Jamie Graybeal, a spokesman for the U.S.-led military coalition.

Graybeal would not describe the concerns, but a report released last week by the New York-based Open Society Foundations said the rift was over whether the Afghans will have a so-called “internment” system that allows some detainees to be held without charge or trial. The U.S. has been holding detainees in internment at Bagram for years.

Although the Afghan government agreed to embrace an internment system by signing the accord in March, some top Afghan officials and legal experts contend it violates the Afghan constitution, the report said. Moreover, Karzai himself is opposed to administrative detention, according to the report.

The U.S. is now worried that the Afghan government will discontinue internment and either release dangerous detainees or forward their cases to the loosely run Afghan judicial system, which is tainted by corruption and secrecy, the group said.

“There are concerns on the U.S. side about division in the Afghan government over internment and that it is not constitutional,” said Rachel Reid, a senior policy adviser on Afghanistan for the Open Society Foundations. “The basic concern is that if they don’t have internment, they will be released.”

On the flip side of the legal issue, some Afghan legal experts are worried about Afghan officials abusing any authority to hold detainees without trial.

“Consider the fact that even our regular laws are ignored by powerful people,” said Abdul Qawi Afzali of the Legal Aid Organization Afghanistan. “What will happen when you give them the actual, legal power to detain people like this law does?”

Panetta, the Pentagon chief, spoke with Karzai by phone Monday and “expressed a shared commitment to implement the terms of the memorandum of understanding on detention operations,” said his press secretary, George Little. He said the phone call was cordial.

Monday was the deadline for the transfer of the prison.

In Brussels, NATO Secretary-General Anders Fogh Rasmussen downplayed the dispute and said the handover reflected the ongoing process of Afghans taking the lead for running security and other institutions in their homeland. Afghan policemen and soldiers are to be in charge of security across the country by the end of 2014, when most international troops will have left or moved into support roles.

“We take it for granted that the Afghan authorities will take all necessary measures to prevent any security risks,” the NATO chief said. “That’s also in their interest.”

Afghan officials also played down the issue.

Acting Defense Minister Enayatullah Nazari said after the ceremony that the delay in handing over the rest of the prisoners was due to “technical issues.”

Farouk, the new prison director, said: “We are telling the Afghan president and the Afghan people that today is a proud day. We will protect the rights of prisoners according to international law and Afghan law.”

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