KABUL, Afghanistan -- U.S. officials handed over formal control of Afghanistan’s only large-scale U.S.-run prison to Kabul on Monday, 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 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.

The 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 Guantánamo 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 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; 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.

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 since the signing of the March 9 handover agreement gradually handed over responsibility for most of the 3,000 detainees held at the prison. 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 Defense Minister Enayatullah Nazari and the army chief of staff.

According to Farouk, 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 impact military operations around Afghanistan.

It is also unlikely to impact 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.