U.S. officials have handed over formal control of Afghanistan's only large-scale U.S.-run prison to Kabul, even as disagreements between the two countries over the thousands of Taliban and terror suspects held there marred the transfer.

The handover ceremony took place Monday at the prison next to a sprawling U.S. airfield in Bagram, just north of Kabul. President Hamid Karzai has called the transfer a victory for Afghan sovereignty.

Shortly after the handover ceremony, a suicide bomber in the northern city of Kunduz killed 15 people and wounded another 25. The bombing came as a stark reminder that the insurgency is waging a ceaseless campaign against the Afghan government and the U.S.-led NATO military alliance, and that many of those held in the prison have been arrested for organizing such attacks.

Enayatullah Khaliq, a spokesman for the Kunduz provincial governor, said the blast took place in the early afternoon. He had no other details. Governor Mohammad Anwar said the bomber was on foot and blew himself up next to a group of police officers.

The Bagram prison, formally known as the Parwan Detention Facility, has been the focus of controversy in the past but never had the notoriety of the prisons at Guantanamo Bay or Abu Ghraib in Iraq.

The prison facility was built about three years ago to replace a holding facility formerly located in an old Soviet hangar inside the base.

Earlier this year, the prison gained unwanted attention when hundreds of Qur'ans 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; six U.S. soldiers were killed during the violent demonstrations.

"We are telling the Afghan president and the Afghan people that today is a proud day," said Afghan army Gen. Ghulam Farouk, who now heads the prison.

The transfer is politically important for Karzai, a member of Afghanistan's Pashtun community who has been trying to assert his authority and counter accusations by Taliban insurgents that he is an American puppet.

Disagreement over detainees

The prison's successful transfer also is seen as a critical part of the U.S. handover of responsibilities for such institutions to the Afghan government by the end of 2014, when most foreign troops leave the country.

The U.S. has gradually handed over responsibility for most of the 3,000 detainees held at the prison since the signing of the March 9 handover agreement. As some may have been released or others brought in, the prison's current detainee population under U.S. control is not known, but is thought to number in the hundreds.

The U.S. recently suspended the transfer of new detainees apparently because of disagreements with Kabul, which has questioned the long-term detention of suspects without charge after their capture.

The U.S. reportedly fears that Afghan authorities may simply let some detainees go, and appears reluctant to turn over all the suspects it holds.

American irritation was apparent at the ceremony, where the U.S. military was represented by 42nd Military Police Brigade Commander Col. Robert Taradash, who runs the facility. No higher ranking American officers went, although the Afghan government sent its Afghan Defence Minister Enayatullah Nazari and the army chief of staff.

According to Farouk, the United States has transferred 3,082 detainees but was still in the process of transferring another 600 captured after the March agreement. The U.S. will also continue to hold about 50 non-Afghan prisoners that are not covered by the agreement on a small part of the facility that they will still administer. They are thought to include Pakistanis and other foreign nationals either captured in Afghanistan or transferred to Bagram from other wars, such as Iraq.

The disagreement indicates the tense relations between the U.S.-led NATO military coalition and Karzai, but is not expected to affect military operations around Afghanistan.

It is also unlikely to affect the gradual handover of security responsibilities from NATO to Afghan forces. The United States and its allies are drawing down their military forces in Afghanistan and hope to fully hand over control to the Afghans by the end of 2014.

Nazari said after a ceremony that "very few prisoners" remained with the United States military and the rest are under Afghan control.

He attributed the delay in handing over the rest to "technical issues," but did not elaborate.

U.S. suspends transfer of 30 detainees

On Sunday, the U.S. also suspended the transfer of about 30 detainees that remained from the original group of about 3,000.

"Some 99 per cent 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.

He said concerns focused on the Afghan government's intentions to implement the March agreement, but would not explain further.

Afghan officials and analysts have said the dispute is over a system of administration detention that allows extended no-trial internment for wartime prisoners. Although this is permitted under the international laws on war, some Afghan officials say it may not be legal under the Afghan constitution.

"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."

Another issue is how quickly Afghans arrested on the battlefield by U.S. forces are handed over to the government.

Foreign Ministry spokesman Janan Mosazai said all Afghan detainees have to be turned over within 72 hours. The U.S. wants to be able to keep detainees longer than that.