Human Rights Watch is suing Israel for ordering the deportation of the group's Israel and Palestine director for allegedly supporting a boycott of the Jewish state.
The Israeli Interior Ministry has revoked Omar Shakir's work permit and has given him 14 days to leave the country.
Human Rights Watch said it would challenge the order in court.
"This is not about Shakir but rather about muzzling Human Rights Watch and shutting down criticism of Israel's rights record," HRW Deputy Director Iain Levine said Tuesday. "Compiling dossiers and deporting human rights defenders is a page out of the Russian or Egyptian security services' playbook."
Israeli Interior Minister Aryeh Deri said Israeli authorities had gathered data on Shakir for more than a decade.
"It is inconceivable that a boycott activist can receive a permit to remain in Israel so that he can act in every possible way against the state," Deri said. "I will use all means to expel such people from the country."
But HRW said neither the group nor its representatives advocate boycotts of Israel. They say the Interior Ministry even acknowledged in its letter revoking Shakir's work permit that "no information has surfaced regarding such activities" since he joined the group.
Israel originally denied Shakir a work permit last year, but relented after, in part, pressure from the United States.