Israel’s interior ministry has ordered the representative of Human Rights Watch in the country to leave within 14 days, accusing him of supporting a boycott against Israel.

Human Rights Watch, a New York-based rights organisation, said the decision showed Israel was seeking to suppress criticism of its human rights record, and that it would challenge the decision in court.

Omar Shakir, the group’s Israel and Palestine Director, holds US citizenship. He has denied the accusation against him.

Israel last year initially denied Shakir a work permit, in a move criticised by the US. It later granted him a one-year work visa.

Israeli interior minister Aryeh Deri said he had acted on the recommendation of Gilad Erdan, the minister for strategic affairs, whose department said it gathered data that Shakir had for years supported a boycott of Israel.

“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. I will use all means to expel such people from the country,” Deri’s statement said.

But Shakir said: “I have not called for any form of boycott of Israel during my time at Human Rights Watch and the interior ministry acknowledged this in its letter to me ... in which they informed me of their decision to deny an extension to my work visa.”

HRW said it supported Shakir. “This is not about Shakir, but rather about muzzling Human Rights Watch and shutting down criticism of Israel’s rights record,” its program director, Iain Levine, said.