The proportion of detainees who reported torture or ill-treatment at facilities run by Afghanistan's main security agency, the National Directorate of Security (NDS), decreased to 19 percent in 2018, from 29 percent in 2016.
Among conflict-related detainees held by the Afghan National Police, the proportion who reported torture or ill-treatment fell to 31 percent from 45 percent.
However, a third of 618 conflict-related detainees interviewed in 77 facilities in 28 provinces in the past two years provided accounts of widespread torture or ill-treatment.
"As our report illustrates, there is still a long way to go to eradicate this horrendous practice among conflict-related detainees," said Tadamichi Yamamoto, the U.N. secretary-general’s Special Representative for Afghanistan.
Officials at the NDS and police were not immediately available for comment.
Afghanistan's U.S.-backed government is holding thousands of detainees, many captured as part of the war with the Taliban and other hardline Islamist groups.
The Taliban have made major gains in recent years and now effectively control half the country.
The U.N. agencies said beating was a common form of torture to force confessions.
Higher incidence of torture was noted at a detention center run by the Afghan National Police in the southern province of Kandahar.
The detainees reported various forms of torture such as suffocation, electric shocks and suspension from ceilings.
Last year, the government committed to the prevention of torture by acceding to the Optional Protocol to the Convention against Torture, and it had made progress in implementing a National Plan on the Elimination of Torture, the agencies said."We welcome the steps taken by the government to prevent and investigate cases of torture and ill-treatment over the past two years," Yamamoto said.