The Justice Ministry said on the official website press-uz.info that these groups, including New York-based Human Rights Watch, have not yet submitted detailed reports on their activities and funding.
It did not specify what measures would be taken.
Alison Gill, the director of HRW's Office for Russia and Central Asia in Moscow, told RFE/RL that her organization was making every effort to comply with the law.
"We always try to strictly keep within the law and [in Uzbekistan] we have also tried to comply with the law," she said. "If the Uzbek government wants to create problems for us, it will do that. In fact, they have already created problems by denying a visa to another [Human Rights Watch] staffer."
Tashkent has forced a number of Western-funded organizations to stop operating in the country in the past months.
(with material from Reuters)