Israel has denied a work permit to a Human Rights Watch researcher, accusing the group of serving as Palestinian propagandists in a move the US-based organisation called an "ominous turn".

Foreign Ministry spokesman Emmanuel Nahshon said the decision had been taken because of HRW's "extreme, hostile anti-Israel agenda which was working at the service of Palestinian propaganda...in a totally biased manner."

The news emerged as Israel faced criticism from the UN Human Rights Council in Geneva over the 18-month jail sentence handed to an Israeli soldier who shot an incapacitated Palestinian assailant in the head. The council called it an "apparent extrajudicial execution of an unarmed man".

UN human rights spokeswoman Ravina Shamdasani said the sentence given to soldier Elor Azaria was "excessively lenient" and part of a "chronic culture of impunity" for Israeli abuse of Palestinians.

Many Israelis, particularly from the right-wing, opposed the prosecution of Azaria for killing Abdel Fattah al-Sharif Elor, who had attacked one of his comrades with a knife.

HRW said it was "disappointing that the Israeli government seems unable or unwilling to distinguish between justified criticisms of its actions and hostile political propaganda".

The organisation had been granted unimpeded access to Israel and the West Bank for three decades. Israel had now joined Cuba, Egypt, North Korea, Sudan, the United Arab Emirates, Uzbekistan, and Venezuela as countries that have impeded its access, HRW said.

In its letter, the Israeli immigration office said the Foreign Ministry had advised it that HRW's work amounted to "Palestinian propaganda under the false banner of human rights".

"Because of this, we recommend denying the permit," it said.

The US State Department said it strongly disagreed with Israel's characterisation of HRW, which it considers a credible human rights organisation.

"Even though we do not agree with all of their assertions or conclusions, given the seriousness of their efforts, we support the importance of the work they do. We reference HRW reports in our own reporting," acting State Department spokesman Mark Toner said.

Israeli spokesman Nahshon said the decision was a one-off and did not represent a change in policy towards NGOs. The HRW representative could enter Israel on a tourist visa and the work visa application may be reconsidered if an appeal is lodged.

Israel has come under renewed international criticism for its expansion of settlements in the occupied West Bank and East Jerusalem, seen as an obstacle to resolving the Israeli-Palestiniam conflict.

The prospects of peace talks, already at a stalemate, were thrown into additional uncertainty this month when new U.S. President Donald Trump appeared to abandoned a long-standing commitment to a two-state solution.