The United States is withholding the transfer of scores of inmates, reportedly out of concern that Afghan authorities may simply let some detainees go and no longer hold dangerous prisoners without charge.
American irritation was apparent at the ceremony at the prison, about 25 miles (40 kilometers) north of Kabul. No higher ranking American officers attended, although the Afghan government sent its defense minister, army chief of staff and other officials.
Karzai also did not attend, though he released a statement calling the handover a "very big step regarding the sovereignty of Afghanistan."
"Now, the Bagram prison is converted to one of Afghanistan's regular prisons where the innocents will be freed and the rest of the prisoners will be sentenced according to the laws of Afghanistan," the statement said.
The more than 2,000 Afghan military policemen now at the prison said the inmates were pleased to be guarded by Afghans.
"We are Afghan and they are Afghan. They are Muslim. We are Muslim," said Ashna Gul, a military policeman from Nangarhar province in eastern Afghanistan. "We can see each other through the steel windows.
Firoz Khan, another military policeman from Nangarhar, said some of the inmates ask him to get them more soap and shampoo.
"We sympathize with them because they are prisoners and they are away from their families," Khan said.
Hours after the handover ceremony, a suicide attack killed 15 people and wounded 25 others in the northern city of Kunduz. The bombing was a stark reminder that insurgents continue their fight against Afghan and U.S.-led coalition troops and that many detainees at the prison are suspected of organizing such attacks.
The U.S. began detention operations at Bagram Air Field in early 2002. For several years, prisoners were kept at a former Soviet aircraft machine plant converted into a lockup. In 2009, the U.S. opened a new detention facility next door. The number of detainees incarcerated at the prison, now called the Parwan Detention Facility, has swelled from about 1,100 in September 2010 to 3,110 in the spring of this year.
The prison has been the focus of controversy in the past but never had the notoriety of the prisons at the U.S. military detention center at Guantanamo Bay, Cuba, or Abu Ghraib in Iraq. Had al-Qaida leader Osama bin Laden been captured instead of killed, CIA Director Leon Panetta said he would have been taken to Bagram first, then probably to Guantanamo Bay.
Earlier this year, the prison gained unwanted attention when hundreds of Qurans and other religious materials were taken from its library and sent to a burn pit at the military base. The event triggered scores of deadly anti-American protests across Afghanistan. More than 30 Afghans and six U.S. soldiers were killed during the violent demonstrations. Karzai said Qurans would never have been burned if Afghans had been in control of the prison then.
Karzai and the United States signed a memorandum of understanding about the future of the detention facility on March 9, following tense negotiations that frequently stalled.
Since then, the U.S. has transferred 3,082 detainees to Afghan control, according to Afghan Army Gen. Ghulam Farouk, who now heads the prison. He said Monday that the U.S. was in the process of transferring the remaining 30 inmates picked up before the memorandum was signed plus another 600 captured after the signing.
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."
There is another major issue that remains unresolved at the prison.
The memorandum of understanding did not address the estimated 50 non-Afghan prisoners that the U.S. is holding at the prison. They include individuals from Pakistan, Tunisia, Yemen and detainees transferred to Bagram from other wars, such as Iraq. The U.S. will retain custody of these non-Afghan prisoners until their fate is addressed in another agreement between the Afghan and U.S. governments.
At the ceremony, 16 prisoners, all wearing matching gray sweaters, were released.
Haji Lalai from Kandahar, the spiritual birthplace of the Taliban, said he was detained at the prison two years—20 months by the U.S. military and four months under Afghan guard.
"It was OK, but sometimes the Americans had a bad attitude against us," he said, adding that he didn't like the prison food and often shivered in his cell. "I am happy to be released. I was not an insurgent. I was innocent. I was arrested in my house."
Mirwais, a man from Zabul province in the south who uses only one name, told a similar story.
"The U.S. raided my home. I'm a shopkeeper. I was at home with my family and they raided my home at night and took me to Bagram," Mirwais said, adding that he was imprisoned for 10 months. "The Americans' attitude toward us was not good."
Riechmann reported from Kabul. Associated Press Writer Patrick Quinn in Kabul also contributed to this report.