In a statement, Human Rights Watch (HRW) said Niyazova has been indicted on politically motivated charges of illegal border crossing, smuggling, and distributing material causing public disorder by using financial support from foreign governments.
HRW says she faces up to 10 years of imprisonment.
Niyazova was detained crossing into Uzbekistan from Kyrgyzstan in December 2006. She was interviewing family members of victims of the violence in the eastern city of Andijon in May 2005 that left at least 189 people dead.
The New York-based group also said Uzbek authorities have denied work accreditation to its Tashkent office director because she had "exceeded her authority" and "worked outside the office charter."
HRW said the moves are the latest steps in the government's crackdown on human rights defenders and civil society.