© ReutersOmar Shakir
Omar Shakir, a US citizen and the watchdog's director for Israel and the Palestinian territories, was accused of supporting boycotts of the country based in part on pro-Palestinian comments he had made in the past.
In July, Mr Shakir lodged an appeal with the Supreme Court against an earlier court decision to revoke his work and residency permit and issue a deportation order.
The lower court initially argued that previous statements Mr Shakir made as a student and his Human Rights Watch (HRW) activities on Israel's West Bank settlements amounted to support for the pro-Palestinian "Boycott, Divestment and Sanctions" (BDS) movement.
HRW have repeatedly denied that either the group or Mr Shakir has called for an outright boycott of Israel.
Israel effectively criminalised support for "BDS" with an amended law in 2017. Mr Shakir's case has therefore been followed closely internationally as a litmus test for how Israel would enforce the controversial anti-BDS legislation.
On Tuesday the Supreme Court issued a unanimous three-judge decision supporting the Israeli government's initial move against Mr Shakir.
His lawyer said Mr Shakir will have to leave the country within 20 days or face deportation.
If he is expelled, he will lose access to Israel and the Palestinian territories, as most entry points are controlled by Israeli security forces.
"They have basically declared free expression in Israel does not include mainstream advocacy for Palestinian rights. This issue is much larger than one person or one organisation or even human rights advocacy at large," he said.
"It goes fundamentally to Israel's commitment to basic democratic values. If the government deports a HRW representative for asking businesses to respect rights, who will they throw out next?" he added.
Back in July HRW's executive director Kenneth Roth told The Independent the case against HRW was a "full-frontal attack on human rights advocacy" and "a slippery slope".
"If the Israeli government can get away with this, what is next? Will they prohibit calling the West Bank occupied or prohibit invoking the International Criminal Court?" he said.
"There are very few governments in the world which bar Human Rights Watch, Israel joins the unsavoury club of the likes of Iran, North Korea, Venezuela and Cuba," he added.
The Supreme Court decision was lauded by Israeli officials.
Israel's interior minister Aryeh Deri said he was "glad" Mr Shakir's appeal had been rejected.
"Let everyone know those who act against the state, we will not allow them to live or work here," he wrote on Twitter.
The country's minister for strategic Affairs, Gilad Erdan, meanwhile said work visas "should not be given to a foreign boycott activist who wants to harm Israel".
"HRW is welcome to appoint another representative in Israel in place of Shakir if it chooses to do so," he added in a statement.
Israel has adopted a tough stance in recent years towards the Palestinian-led BDS movement which it says is aimed at delegitimising Israel's existence and wiping it off the map.
The BDS movement presents itself as a non-violent campaign for Palestinian rights and says it does not endorse a specific solution to the conflict.
The case against Mr Shakir was first triggered in May 2018 by an Israeli interior ministry decision to revoke his work permit on the basis that he had "continuously" called for boycotts of Israel, citing his student activism dating back to 2006 before he joined HRW, as well as his subsequent work for the group.
The dossier also listed HRW's recent research in which it recommended global tourism companies like Airbnb halt operations within Israeli settlements in the occupied West Bank, as they are illegal under international law.
Israel's anti-boycott law does not distinguish between boycotts directed at Israel and those directed at only West Bank settlements.
The government decision to revoke his work and residency visa was approved in April by the Jerusalem District Court, prompting HRW to lodge an appeal.
In July Amnesty International and a group of former Israeli ambassadors joined the legal case arguing in an "amicus curiae" (friend of the court) briefing that expelling Mr Shakir was "an unreasonable and disproportionate restriction on the rights to freedom of expression and association".
At the time they called the deportation order "a crushing blow to freedom of expression in the country" and "an alarming signal" to rights groups.
The decision has also faced criticism from within Israel.
Leading Israeli rights group B'Tselem said that the decision does not reflect the rule of law "but legal propaganda at the service of the occupation".
"In essence, the HCJ's ruling grants a legal seal of approval to the further shrinking of the already limited space in Israel to oppose the occupation. For decades, this space is non-existent for Palestinians; now, it will be diminished further for international stakeholders; and soon, also for Israelis," added Hagai El-Ad, B'Tselem's executive director.
However pro-Israel lobbying group "NGO Monitor", which joined the legal case in support of the state, said Mr Shakir had "vilified" Israel, and heralded Tuesday's decision as "an important expression of Israeli democracy".
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