The report, by Sharif Bassiouni, said Afghanistan was the scene of "gross violations of fundamental human rights", from extrajudicial executions to abuse of women and girls.
The report released on Monday noted "problems of security in a country that is still dominated by the military power of warlords and local commanders and by the rising economic power of those who are engaged in poppy cultivation and heroin traffic".
Bassiouni also highlighted deplorable conditions at Pol-e-Charkhi prison, where, he said 734 Pakistanis and Afghans had been detained illegally for 30 months, awaiting release by President Hamid Karzai.
Conditions in the prison must be improved to meet UN minimum standards, he said.
The report made about 30 recommendations, among them: The release of all persons detained for long periods without charges; a ban on marrying off girls as a means of satisfying blood feuds or debts; means to stop the trafficking of infants; and fighting the drug trade.