The head of a UN inquiry into last summer’s Israeli military offensive in Gaza has said he will resign after Israeli allegations of bias due to consultancy work he did for the Palestine Liberation Organisation (PLO).

William Schabas, a Canadian academic, was appointed last August by the head of the UN Human Rights Council to lead a three-member group looking into alleged war crimes during the offensive.

In a letter to the commission, a copy of which was seen by Reuters, Schabas said he would step down immediately to prevent the issue from overshadowing the preparation of the report and its findings, which are due to be published in March.

Schabas’ departure highlights the sensitivity of the UN investigation just weeks after prosecutors at the international criminal court in The Hague said they had started a preliminary inquiry into alleged atrocities in the Palestinian territories.

In the letter, Schabas said a legal opinion he wrote for the PLO in 2012, for which he was paid $1,300 (£900), was not different from advice he had given to many other governments and organisations.

“My views on Israel and Palestine as well as on many other issues were well known and very public,” he wrote. “This work in defence of human rights appears to have made me a huge target for malicious attacks.”

Israel had long criticised Schabas’ appointment, citing his record as a strong critic of the Jewish state and its current political leadership. Schabas said his work for the PLO had prompted the Human Rights Council’s executive to seek legal advice about his position from UN headquarters on Monday.

“I believe that it is difficult for the work to continue while a procedure is underway to consider whether the chair of the commission should be removed,” he wrote.

The commission had largely finished gathering evidence and had begun writing the report, he added.

On Tuesday morning Israel’s prime minister, Binyamin Netanyahu, called for the UN investigation to be scrapped, calling it an “anti-Israeli body” that has proved it has nothing to do with human rights.

“This is the same council that in 2014 made more decisions against Israel than against Iran, Syria and North Korea combined,” Netanyahu said, adding that Gaza’s Hamas rulers “need to be investigated, not Israel”.

The commission is looking into the behaviour of both the Israelis and of Hamas, the Islamist movement that controls Gaza and calls for the destruction of Israel.

The appointment of Schabas, who lives in Britain and teaches international law at Middlesex University, was welcomed at the time by Hamas but was harshly criticised by Jewish groups in the US.

Schabas had said at the time he was determined to put aside any views about “things that have gone on in the past”.