The campaign group Human Rights Watch says the Uzbek government continues to persecute people connected to unrest in Andijan three years ago.
Officials are using threats and torture to silence witnesses to the killings, the New York-based organisation says.
According to survivors, hundreds of people died when armed forced fired at largely peaceful protesters.
The Uzbek government has denied there was a massacre of civilians, saying it thwarted an Islamic uprising.
The BBC's Monica Whitlock, who reported on the events in Andijan in May 2005 says the report fills in some of the silence that followed the killings.
It details what it says is an attempt by the Uzbek government to intimidate witnesses.
Many have been tortured, threatened with rape and subjected to repeated humiliation, including being forced to crawl like a dog during police interrogation, the report says.
All are under constant surveillance by the secret police, it adds.
The report draws on the testimony of refugees who fled after the shooting.
It describes how those trying to make new lives abroad are pressed to return home - or risk further consequences for their families.
"The government wants to get everyone back to Uzbekistan to save its secrets," one man told Human Rights Watch.
The violence at Andijan broke out after an armed jail-break turned into a huge demonstration involving thousands of ordinary Uzbeks.
The government says the protestors wanted to stage an Islamic coup.
It says the death toll was exaggerated, and that nearly all of those who died were soldiers or terrorists
Tashkent has not allowed an international inquiry.
Foreigners are barred from talking to residents in Andijan or to visit the burial grounds outside the city.