Downing Street has changed its explanation for David Cameron's resignation as honorary patron of JNF.
Mr Cameron is now the first British prime minister not to be patron of the charity in the 110 years of its existence.
His office initially said that a review of all his links with charities had been made when the coalition was formed in May last year, and a number were dropped due to "time constraints" - as reported in the JC last week.
But this week a spokesman confirmed that the reason was JNF's links to Israel.
He said: "We first discussed this with JNF late last year and had a conversation with them to explain the reasons for this taking place.
"We had to think about what organisations the prime minister could have an official involvement with. One of the issues was having an organisation that was specifically focused around work in one specific country. We spoke to JNF to say this had nothing to do with a policy issue and was based around the fact he is now prime minister rather than leader of the opposition."
The spokesman said a "handful" of other organisations were also dropped, including one other with links to a specific country. But Downing Street has refused to name any of the others affected.
"This has absolutely nothing to do with any anti-Israel campaign," he added. "The Prime Minister's clear views on Israel are on record."
Tony Blair and Gordon Brown remain patrons of JNF.
A leading Jewish figure in the Conservative Party confirmed this week that he had advised Mr Cameron to drop JNF because there were better Jewish causes to support. He said there was no reason to continue as patron "simply because other PMs have been".
But the former JNF president, Gail Seal, said: "I'm extremely concerned this has happened now. It is very damaging, not just for JNF but for the community. It undermines the work we are trying to do for Israel.
"It's broken a chain since 1901 where we have always had a British prime minister as a patron. It's very sad and I'm very upset about it.
"We always had a very close relationship with Downing Street and great respect for our patrons. We were a very successful organisation and always got on brilliantly. I don't know what has happened since I left three years ago."
Harvey Rose, chairman of the Zionist Federation, said the decision sent a "terrible message" to Israel supporters in the UK.
"It is also a slap in the face to the Jewish community in the UK, whose relationship with the JNF was historically a hugely important part of their Jewish identity and their connection to Israel," he said. "The Jewish community has given so much to this country and deserves more sensitive treatment than this."
Freddie Knoller, a 90-year-old Auschwitz survivor from north London, said he was "very upset" at the decision.
But Stuart Polak, director of Conservative Friends of Israel, said the move was being "blown out of proportion".
He said: "Jumping to conclusions without the full facts can be dangerous at worst and mischievous at best.
"The Prime Minister's support for and understanding of Israel speaks for itself, whether in the House of Commons, in speeches - like to CST earlier this year - or in private meetings with PM Netanyahu, the last one being only two weeks ago. We are fortunate to have a Prime Minister committed to the state of Israel.
"Judgments on the government's support for and understanding of Israel should be based upon substantive and serious matters, not on a decision which is clearly part of a wider rationalisation affecting several charities and outside organisations."
JNF declined to comment.