The panel's findings were the result of a two-week fact-finding mission following a U.N. report last month that said Afghan authorities are still torturing prisoners despite promises of reforms. The country's intelligence service earlier had denied any torture in its detention facilities.
The complaints have prompted NATO to stop many transfers of detainees to the Afghans as concerns about torture raise questions about the government's commitment to human rights.
The U.N. report said more than half of the 635 detainees interviewed had been tortured - about the same ratio found in its first report in 2011. It cited brutal tactics including hanging detainees from the ceiling by their wrists, beating them with cables and administering electric shocks.
Many rights activists have expressed concern that such abuses could become more common as international forces draw down and the country's Western allies become less watchful over a government that so far has taken few concrete actions to reform the system.
The Afghan panel also denied the allegation in the U.N. report that the government appeared to be trying to hide the mistreatment by hiding detainees in secret locations during inspections by international observers.
Commission head Abdul Qadir Adalatkhwa told reporters that torture and beatings occur in the first stages of the arrest "but not while they are in prison."
The delegation visited both male and female prisons as well as juvenile detention facilities.
Adalatkhwa said 148 of 284 prisoners interviewed in the provinces of Kabul, Kandahar and Herat complained of torture and misbehavior at the time of their arrest and during the interrogation period. Of those 136 cases were confirmed, he said. The panel also interviewed 23 female detainees and found no confirmed allegations of rape and abuses.
He also said more than 66 percent of those interviewed also had no access to defense lawyers.
The government-appointed commission plans to discuss the findings during a meeting with judicial officials and President Hamid Karzai later this week at the presidential palace, Adalatkhwa said.
"There is no systematic torture in Afghan detention centers," he said.
In a letter responding to the U.N. report, Gen. John Allen, the then-commander of U.S. and NATO forces in Afghanistan, said his staff had written letters to Afghan ministers urging them to investigate more than 80 separate allegations of detainee abuse during the past 18 months.
"To date, Afghan officials have acted in only one instance," Allen said in the letter. In that case Afghan authorities did not fire the official in question, but transferred him from Kandahar province to Sar-e-Pul in the north.
The letter said the NATO military alliance had responded to the U.N. report by stopping transfers of detainees to seven facilities in Kabul, Laghman, Herat, Khost and Kunduz provinces - most of them the same facilities that were flagged a year ago.
The transfers were halted in October, when the U.N. shared its preliminary findings with the military coalition.
"We have only stopped transferring some detainees to certain Afghan facilities," Jamie Graybeal, a spokesman for the international military alliance in Kabul. "The Afghan government has stated its commitment to upholding its human rights obligations and we remain committed to working together with the International Community to support them in their efforts to tackle this difficult problem. "