A US military spokesman said on Monday Brig Gen Charles Jacoby started the review, which was announced last week, with visits to two bases in border areas dogged by attacks by armed fighters.
"Gen Jacoby is now into about the third day of the top-to-bottom review of all the coalition's detainee facilities and procedures," said Lt Col Tucker Mansager, a spokesman for US forces in Afghanistan.
The military says Jacoby, the deputy operational commander at the main US base at Bagram, north of Kabul, is to visit about 20 US holding facilities around the country, including the principal jail at Bagram, "to ensure internationally accepted standards of handling detainees are being met".
The spokesman declined to identify the first two bases visited, but said they were in eastern Afghanistan.
The military recently announced two new criminal investigations into ex-inmates' allegations of abuse - including a former Afghan police colonel's claim he was beaten and sexually abused in mid-2003 and released without charge.
But the army's criminal investigations into the deaths of two Bagram inmates in December 2002 have dragged on for more than a year. Both were ruled homicides after military autopsies and prompted undisclosed changes to prison procedures.
Many prisoners in Afghanistan
were transferred to Guantanamo
Mansager said he could not confirm a New York Times report that a military intelligence unit that oversaw interrogations at Baghdad's Abu Ghraib prison - the focus of the Iraqi prisoner abuse scandal - was also in charge of questioning at the Bagram detention centre when the two prisoners died.
Interrogations at the centre, known as the Bagram Collection Point, were supervised by Company A, 519th Military Intelligence Battalion, which moved to Iraq in early 2003, the paper said, citing information from former prisoners, military officials and documents.
Mansager said members of the 519th were deployed in Afghanistan between November 2003 and March 2004. "Other than that, we don't know their assignment history," he said.
US-led forces have detained hundreds of people in Afghanistan since ousting the Taliban in late 2001 for harbouring Usama bin Ladin and his al-Qaida network.
The US considers them "unlawful combatants" not entitled to the full protection of the Geneva Conventions, and many have been transferred to Guantanamo Bay, Cuba, and held without trial or access to lawyers for more than two years.
The CIA inspector general is investigating the death of another detainee in Afghanistan's eastern Kunar province in June 2003.
Rights groups have long complained that US authorities have failed to dispel lingering allegations of abuse in Afghanistan - concerns that could fuel sympathy for fighters mounting attacks despite the presence of 20,000 US-led troops and 6000 peacekeepers in Kabul.