Capt. Kirk Black, who trains the Afghan police in this impoverished province, developed a practiced skepticism about claims of innocence during a decade as a Baltimore police officer.

But last January, when relatives of an Afghan imprisoned at the Bagram military detention center begged him to look into the case, he agreed to listen. Eventually he became convinced that the detention was a case of mistaken identity and put the family in touch with a lawyer.

Soon, Captain Black was facing a potential legal battle of his own. One of his senior commanders ordered him not to discuss the case, and the military sent an officer to investigate him. He retained military defense counsel.

The Bagram prison — where about 600 people, mostly Afghans, are being held indefinitely and without charges — is a delicate issue for the Obama administration at a time when it is struggling to come up with a plan for detainees in the prison at Guantánamo Bay, Cuba, which it intends to close.

The administration has argued that military detainees in Afghanistan may not challenge their detentions in American courts. A federal judge ruled last month that some Bagram detainees captured outside Afghanistan had the constitutional right of habeas corpus, citing a Supreme Court ruling. But the new administration has appealed.

Captain Black’s involvement in the Bagram detainee’s case began in January, while the American officer was attending a meeting of village elders and leaders. He was approached by relatives of an Afghan named Gul Khan, who they said had been snatched by American troops in September and imprisoned at Bagram Air Field, north of Kabul. The military apparently believed Mr. Khan was a Taliban leader named Qari Idris. But local Afghan officials told Captain Black it was a case of mistaken identity. Captain Black, believing that he was fulfilling a policy of the American counterinsurgency by trying to hear out locals with grievances, applied his police training to the evidence he heard.

“Upon speaking to multiple village elders, family members, the police chief and the subgovernor, I am convinced that the individual in question is not the person that the government claims,” he wrote in January to Clive Stafford Smith, a human rights lawyer he had met three years earlier during a posting to Guantánamo. “I am a police officer in the United States, and there is a mass of evidence that this individual does not need to be held.”

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Captain Black, 36, who grew up in the Detroit suburbs and attended college in Michigan, joined the Baltimore police force in 1999. He eventually became a member of its SWAT team.

In 2006 he was deployed to Guantánamo as an Army National Guard officer. “When I got there, I’ll admit I basically believed everyone there was a terrorist and we had every right to be holding them,” he said. “But as I learned more about the system, I learned that quite a few of them were just swept up in the initial invasion.” He also said he and some fellow officers grew to fear that harmless or innocent detainees were locked away alongside hard-core jihadists and were vulnerable to conversion.

Late last year, Captain Black was sent to Ghazni Province. He and his fellow officers said they soon ran into limits on how much they could accomplish. The biggest frustration: provincial government and police officials so steeped in corruption that they seemed to knock the Americans back every time they tried to take a step forward.

Hearing out Mr. Khan’s family, which had the support of police and other village leaders, struck Captain Black as a way to build trust and show that the military would look into complaints of wrongful incarceration.

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In March, Captain Black said, he was ordered by a commander several rungs above him to “toe the party line” and not discuss Mr. Khan’s guilt or innocence. He was also ordered not to allow two journalists who visited his base to accompany him on routine trips to Waghez.

A few days later, as part of an official military investigation, a more senior officer unexpectedly arrived at Captain Black’s base to question him about conversations with Mr. Khan’s family and with this reporter. The investigating officer also sought a sworn statement from this reporter, who declined.

A military spokesman in Kabul did not respond to questions about why the decision was made to investigate the captain — or whether he would be punished. American military officials in Afghanistan and Washington also declined to comment about evidence against Mr. Khan. One official would say only that all Bagram prisoners were classified as “an imminent danger to the lives of U.S. service members.”

Citing his orders, Captain Black declined to comment about specifics of Mr. Khan’s case. But in an interview before those orders were issued, he said he was mindful of the danger of incarcerating someone who might be innocent. “Lock a guy down for 22 hours a day,” he said, “and you are creating a criminal.”