JERUSALEM — An advocate for Human Rights Watch must leave the country by May 1, an Israeli court ruled on Tuesday, upholding a deportation order issued under a contentious law that bars entry to foreigners who have publicly called for a boycott of Israel or its settlements in the occupied West Bank.

The deportation order against Omar Shakir, an American citizen and the organization’s Israel and Palestine director, is the first application of the law against a person lawfully present in Israel.

The case against Mr. Shakir comes as part of a broader Israeli clampdown against the international movement to boycott Israel, a campaign that the government, empowered by the staunch support of President Trump, says delegitimizes the country and smacks of anti-Semitism.

Activists defend the movement as a nonviolent means to protest Israel and its policies toward Palestinians, along with its settlements, which most of the world considers to be a violation of international law. Last week, the United States barred entry to Omar Barghouti, one of the co-founders of the Boycott, Divestment and Sanctions movement, also known as B.D.S., without explanation.

Human Rights Watch, which is based in New York, said it would file an appeal with Israel’s Supreme Court. The Jerusalem District Court said its May 1 deadline would not be enforced pending an injunction and resolution of the appeal.

“Israel portrays itself as the region’s only democracy, but is set to deport a rights defender over his peaceful advocacy,” Tom Porteous, deputy program director at Human Rights Watch, said in a statement.

The Israeli authorities have accused Human Rights Watch of anti-Israel bias in the past and compiled a dossier on Mr. Shakir documenting his activities in support of a boycott, mostly from before he joined the advocacy group.

Like the dossier, the Jerusalem District Court ruling also pointed to reports and advocacy by Human Rights Watch that called on businesses to cease activities that benefit Jewish settlements in the occupied West Bank.

The judgment cited recent Twitter posts written by Mr. Shakir, including some promoting a decision by Airbnb to stop listing properties in West Bank settlements — a decision Airbnb has since reversed.

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“The decision sends the chilling message that those who criticize the involvement of businesses in serious abuses in Israeli settlements risk being barred from Israel and the Israeli-occupied West Bank,” Mr. Porteous said.

Human Rights Watch described Tuesday’s decision as “a new and dangerous interpretation” of the entry law.

In her ruling on Tuesday, Judge Tamar Bazak-Rappaport of the district court wrote, “It has been proven that the petitioner continues to call publicly for a boycott against the state of Israel or parts within it, and in the same breath requests that it will open its gates to him.”

The decision came the same day that a Jewish-American board member of an organization that promotes cooperation between Jewish and Arab citizens of Israel was questioned at length on her way out of the country.

The organization, the Abraham Initiatives, said the authorities at Ben-Gurion International Airport had tried to use “intimidation” against its board member, Laura Mandel, writing in a Twitter post, “We will continue to work for a shared and inclusive Israel, free from discrimination against Arab citizens and those who support #Shared_Society.”

Last year, Israel’s Supreme Court ordered the government to permit entry to an American woman, Lara Alqasem, who arrived with a valid student visa, overruling the Interior Ministry, which had sought to deport her because of her pro-Palestinian advocacy while she was an undergraduate at the University of Florida.

The Israeli government has also sought to curb the activities of Israeli nongovernmental organizations that have been critical of the country’s policies toward Palestinians.

One of them, B’Tselem, the Israeli Information Center for Human Rights in the Occupied Territories, issued a statement on Tuesday in support of Mr. Shakir.

“The government,” it said, “seems to expect all those arriving in Israel to swear allegiance to its policy of endless occupation, settlements and blockade, basically stating: Take it, or leave.”

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