Nearly 300 people were killed in the clashes bewteen the Kyrgyz majority and Uzbek minority in June.
Pillay said her sources indicated that more than 1,000 people had been detained in the southern Kyrgyzstan cities of Osh and Jalalabad since the violence.
There were reports of "sustained, or repeated beatings" of detainees, while those held were also asked to confess to crimes that they claim not to have committed, she said.
Others were released only upon payment of large sums of money while victims' lawyers and families are also being "threatened and intimidated to an alarming degree."
"There are also accounts of detainees being beaten, punched or kicked until they sing the Kyrgyz national anthem perfectly or speak some sentences in Kyrgyz without any trace of 'foreign'"
"Many victims and their families are believed not to be reporting illegal acts by the authorities, and lawyers and human rights defenders who have tried to seek justice have been directly threatened, and in some cases detained themselves," Pillay said.
"The current situation underscores the need for on-going monitoring of the human rights situation, especially in the south."
The allegations of torture and other abuses were made by the staff of international and local aid agencies in the city of Osh and direct witnesses across the south.
Rupert Colville, Pillay's spokesman, said that "the torture goes considerably beyond beatings".
He pointed out a case in which a man died "reportedly as a result of the ill treatment received during the detention."
Reports also indicated that "people have finger nails removed, sharpened sticks inserted between the finger nails and the flesh, asphyxiation, burning cigarettes, beating by rubber batons or rifle butts, punching, kicking etc," Colville said.
"There are also accounts of detainees being beaten, punched or kicked until they sing the Kyrgyz national anthem perfectly or speak some sentences in Kyrgyz without any trace of 'foreign' ie. Uzbek accent."
The ethnic clashes broke out shortly after Kurmankek Bakiyev, the president, was forced from power in a bloodless coup. The interim government has blamed Bakiyev's followers for inciting the violence.