More than 100 non-governmental groups have sent a letter to Kyrgyzstan's president and prime minister to protest against a plan to supervise them.
Justice Minister Marat Kaipov announced the plan last week, citing threats of Islamic terrorism.
Russia recently formulated a law on supervising its own NGOs, which is due to take effect in April.
Most NGOs in Kyrgyzstan have received foreign funding, and the state media portrays them as agents of the West.
"An information campaign is being led against us with the aim of showing that civil society is a puppet of the West," Edil Baisalov, who heads the high-profile NGO Coalition for Democracy and Civil Society, told AFP news agency.
The aim of the supervision, which will be carried out in conjunction with the national security service and the chief prosecutor's office, will check whether an NGO's activities correspond with its charter, Kumar Bekbolotov, director of the Institute for War and Peace Reporting (IWPR) told the BBC News website.
"When the intention is declared in such a general manner... I think NGOs' concerns are justified," he said.
Asiya Sasykbaeva of the Interbilim group told the IWPR: "It is a bad signal for us. If civil society is pressured, it will result in nothing good - it could mean a repeat of the events of March 24," - a reference to the day former President Askar Akayev was driven from power by popular protests.