A UNAMA report said the violations were targeted at a number of groups, including those associated with the ousted government, human rights defenders and journalists. Women's rights had also been eroded, it said.
"UNAMA is concerned about the impunity with which members of the de facto authorities appear to have carried out human rights violations," it said in a statement.
The term "de facto authorities" refers to the Taliban administration which took over Afghanistan in August last year after foreign forces withdrew and the elected government collapsed.
A spokesman for the Taliban government rejected the report's findings, calling them baseless.
"Arbitrary arrests and extrajudicial killing are not allowed," Zabihullah Mujahid said on Twitter. Anyone found guilty of such violations will be considered a criminal and will be dealt with according to Sharia law, he said.
Taliban officials have in the past said retribution attacks were not happening with their leadership's consent and that they had barred fighters from such actions. They also said they had begun a process of purging their ranks of elements that did not fully follow instructions.
While the statement acknowledged steps taken by Taliban authorities apparently aimed at protecting human rights, as well as a "significant reduction in armed violence", it said authorities also bear responsibility.
UNAMA particularly mentioned the role of two bodies in violations - the Ministry of Propagation of Virtue and Prevention of Vice as well as the General Directorate of Intelligence.
The report said the hardest hit victims were those associated with the former government and its security forces.
It listed 160 extrajudicial killings, 178 arbitrary arrests, and 56 instances of torture and ill-treatment of former government employees.
Human rights violations also affected 173 journalists and media workers, 163 of which were attributed to Taliban authorities, including 122 arbitrary arrests and 33 instances of threats.
UNAMA also stressed the erosion of women’s rights.
"Women and girls have progressively had their rights to fully participate in education, the workplace and other aspects of public and daily life restricted and in many cases completely taken away."
UNAMA recorded 2,106 civilian casualties - 700 killed, 1,406 wounded - since the Taliban takeover. A majority were attributed to a local affiliate of the Islamic State militant group.