BAGRAM AIR BASE, Afghanistan — A sweeping United States military review calls for overhauling the troubled American-run prison here as well as the entire Afghan jail and judicial systems, a reaction to worries that abuses and militant recruiting within the prisons are helping to strengthen the Taliban.

In a further sign of high-level concern over detention practices, Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, sent a confidential message last week to all of the military service chiefs and senior field commanders asking them to redouble their efforts to alert troops to the importance of treating detainees properly.

Security lights illuminate the landscape of Bagram Air Base, where terror suspects are held but also where harsh interrogations have been practiced. (Spencer Platt/Getty Images) The prison at this air base north of Kabul has become an ominous symbol for Afghans — a place where harsh interrogation methods and sleep deprivation were used routinely in its early years, and where two Afghan detainees died in 2002 after being beaten by American soldiers and hung by their arms from the ceiling of isolation cells.

Bagram also became a holding site for terrorism suspects captured outside Afghanistan and Iraq.

But even as treatment at Bagram improved in recent years, conditions worsened in the larger Afghan-run prison network, which houses more than 15,000 detainees at three dozen overcrowded and often violent sites. The country’s deeply flawed judicial system affords prisoners virtually no legal protections, human rights advocates say.

“Throughout Afghanistan, Afghans are arbitrarily detained by police, prosecutors, judges and detention center officials with alarming regularity,” the United Nations Assistance Mission in Afghanistan said in a report in January.

To help address these problems, Maj. Gen. Douglas M. Stone of the Marines, credited with successfully revamping American detention practices in Iraq, was assigned to review all detention issues in Afghanistan.

General Stone’s report, which has not been made public but is circulating among senior American officials, recommends separating extremist militants from more moderate detainees instead of having them mixed together as they are now, according to two American officials who have read or been briefed on his report.

Under the new approach, the United States would help build and finance a new Afghan-run prison for the hard-core extremists who are now using the poorly run Afghan corrections system as a camp to train petty thieves and other common criminals to be deadly militants, the American officials said.

The remaining inmates would be taught vocational skills and offered other classes, and they would be taught about moderate Islam with the aim of reintegrating them into society, said the officials, who spoke on condition of anonymity because the review’s findings had not been publicly disclosed. The review also presses for training new Afghan prison guards, prosecutors and judges.

The recommendations come as American officials express fears that the notoriously overcrowded Afghan-run prisons will be overwhelmed by waves of new prisoners captured in the American-led offensive in southern Afghanistan, where thousands of Marines are battling Taliban fighters.

President Obama signed an executive order in January to review policy options for detention, interrogation and rendition.

The Defense and Justice Departments are leading two government task forces studying those issues and are scheduled to deliver reports to the president on Tuesday.

But administration officials said Sunday that the task forces — which are grappling with questions like whether terrorism suspects should be turned over to other countries and how to deal with detainees who are thought to be dangerous but who cannot be brought to trial — were likely to seek extensions on some contentious issues.

Last month The Wall Street Journal reported elements of General Stone’s review, but in recent days American military officials provided a more detailed description of the report’s scope, findings and recommendations.

A spokesman for the Afghan Embassy in Washington, Martin Austermuhle, said he was unaware of the review, and did not know if the government in Kabul had been apprised of it.

Admiral Mullen felt compelled to issue his message last week after viewing photographs documenting abuse of prisoners in Iraq and Afghanistan by American military personnel in the early years of the wars there, a senior military official said.

Mr. Obama decided in May not to make the photographs public, warning that the images could ignite a deadly backlash against American troops.

The admiral urged top American field commanders to step up their efforts to ensure that prisoners were treated properly both at the point of capture and in military prisons.

He told the service chiefs to emphasize detainee treatment when preparing and training troops who deploy to the Middle East and Southwest Asia.

“It is essential to who we are as a fighting force that we get this right,” Admiral Mullen said in the message. “We are better than what I saw in those pictures.”

American officials say many of the changes that General Stone’s review recommends for Bagram are already in the works as part of the scheduled opening this fall of a 40-acre replacement complex that officials say will accommodate about 600 detainees in a more modern and humane setting.

The problems at the existing American-run prison, the Bagram Theater Internment Facility, have been well documented.

The prison is a converted aircraft hangar that still holds some of the decrepit aircraft-repair machinery left by the Soviet troops who occupied the country in the 1980s.

Military personnel who know Bagram and the prison at Guantánamo Bay, Cuba, describe the Afghan site as tougher and more spartan.

The prisoners have fewer privileges and virtually no access to lawyers or the judicial process. Many are still held communally in big cages.

In the past two weeks, prisoners have refused to leave their cells to protest their indefinite imprisonment.

In 2005, the Bush administration began trying to scale back American involvement in detention operations in Afghanistan, mainly by transferring Bagram prisoners to an American-financed high-security prison outside of Kabul guarded by American-trained Afghan soldiers.

But United States officials conceded that the new Afghan block, at Pul-i-Charkhi prison, could not absorb all the Bagram prisoners. It now holds about 4,300 detainees, including some 360 from Bagram or Guantánamo Bay, Afghan prison officials said.

Officials from the general directorate for prisons complained about the lack of detention space based on international standards in provinces of Afghanistan. They said most of those prisons were rented houses and not suitable for detention.

Gen. Safiullah Safi, commander of the Afghan National Army brigade responsible for the section of Pul-i-Charkhi that holds the transferred inmates from Bagram and Guantánamo Bay, said his part of the prison had maintained good order and followed Islamic cultural customs.

But last December, detainees in the other blocks of the prison staged a revolt in an attempt to resist a security sweep for hidden weapons and cellphones. Eight inmates died.

“There’s a general concern that the Afghan national prisons need to be rehabilitated,” said Sahr MuhammedAlly, a senior associate for law and security at Human Rights First, an advocacy group that is to issue its own report on Bagram on Wednesday.