Officials said the release could jeopardize U.S. aid to Afghanistan and worsen already fragile relations between Washington and Kabul, the Wall Street Journal reported.
U.S. officials had urged Kabul not to release suspected insurgent detainees, saying they likely would rejoin Taliban operations.
Abdul Shakor Dadras, a member of the Afghan panel that reviewed detainee case files, confirmed 65 detainees' release on Thursday. Dadras earlier told the Journal the release followed a "long investigation" by Afghan authorities.
Concerning the possibility some of the released detainees would rejoin the insurgency, Dadras said: "Given the kind of geography Afghanistan has, nobody can guarantee who will join with the Taliban or the Afghan government once they are released."
The U.S. military in Afghanistan said some of the freed detainees were "directly linked" to operations in which 32 American or coalition service members were killed or wounded and 23 Afghan security personnel or civilians died or were injured, CNN reported.
The U.S. Embassy in Kabul called the release "deeply regrettable" and said the Afghan government "bears responsibility for the results of its decision."
In a statement before the release, U.S. Forces-Afghanistan said the detainees should be referred for prosecution in Afghanistan.
"Violent criminals who harm Afghans and threaten the peace and security of Afghanistan should face justice in the Afghan courts, where a fair and transparent trial would determine their guilt or innocence," the statement read.
Releasing the detainees violates agreements between the United States and Afghanistan and is "a major step backward for the rule of law in Afghanistan," the statement said.
Afghan President Hamid Karzai already had angered U.S. policymakers by refusing to sign a bilateral security agreement that would allow the United States and its allies to maintain a military presence in Afghanistan to conduct training and counter-terrorism missions after withdrawal of coalition forces at the end of the year.
U.S. lawmakers have said the release of the detainees may jeopardize aid to Afghanistan, which depends on donor assistance to fund government operations and the salaries for army and police.
The 65 prisoners are from a group of 88 detainees the Afghan government had decided to release. Afghan authorities have already released hundreds of prisoners since the Bagram prison near Kabul, once a U.S. prison, was handed over to Afghanistan in March 2013. The facility is now called the Afghan National Detention Facility at Parwan.
In Washington, U.S. State Department deputy spokeswoman Marie Harf, in her media briefing Wednesday, said the 65 detainees are "dangerous" and pose threats to the safety and security of the Afghan people and the Afghan state.
"There is information linking each of them to terror-related crimes, including the use of improvised explosive devices," she said.
Harf said the United States has been concerned because of how the prisoners' cases were considered by the Afghan criminal justice system.