The Turan agency is a rare voice of dissent in the tightly-controlled Caspian Sea nation and has not shied away from critical reporting of the government of strongman leader Ilham Aliyev.
Turan's director Mehman Aliyev said the move was part of a criminal probe into an alleged USD 22,000 in unpaid taxes, a charge he said was false.
"Our bank accounts have been frozen and Turan risks closure at any moment," Aliyev told AFP.
Human Rights Watch denounced the case as the "latest in a vicious crackdown on critical media" in energy-rich Azerbaijan.
The authorities in oil-rich Azerbaijan have faced strong international criticism over claims they routinely harass and jail Aliyev's opponents on trumped up charges, allegations officials deny.
Azerbaijan ranked 162 out of 180 countries in the 2017 World Press Freedom Index released by Reporters Without Borders.
Aliyev took over in 2003 after the death of his father Heydar Aliyev, a former KGB officer and communist-era leader who had ruled Azerbaijan with an iron fist since 1993.
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