The Jewish Chronicle has apologised to readers who complained after it ran an advert for the Disasters Emergency Committee's Gaza crisis appeal.
The weekly newspaper said running the advert was "meant as a purely humanitarian gesture".
When it launched the appeal, the DEC said the latest conflict had made half a million people in Gaza homeless and warned of a "humanitarian emergency".
There is currently a five-day ceasefire between Israel and the Palestinians.
The Israelis launched a military operation on 8 July to stop militant attacks from Gaza.
After a DEC advert featured in this week's Jewish Chronicle (JC), a Facebook page was set up calling on readers to boycott the title until it issued a "full apology".
It accused the newspaper of "ignoring the sensitivity of this conflict which is having a day to day impact and effect on the Jewish community here".
"We have nothing against giving aid to people caught up in a conflict" it said, but accused the Hamas rulers of Gaza of using aid in a campaign of violence against Israel.
A message posted on the paper's own Facebook page pointed out that the advert was "not an expression of the JC's view".
It added: "We have received complaints from readers angry at the decision. We apologise for the upset caused."
It said it would give space in the next issue to readers wanting to object to the advert.
One reader replied: "Maybe you should donate the money you received from this diabolical advert to a pro Israel cause too. Utterly disgraceful."
Others supported the decision to run the DEC advert, however, saying it was the "right thing to do".
Writing on the JC website, editor Stephen Pollard said: "It is a critical part of our editorial independence that we do not allow advertisers to have any influence at all on the paper.
"The ad was approved by the chairman of the JC, who has no involvement in editorial decisions, as an ad for humanitarian aid which nowhere makes political or partisan points."
Meanwhile, Israel's embassy in the UK issued a statement in which it said its own concern about the DEC appeal "stems from the fact that the list of charities on the DEC includes Islamic Relief Worldwide, which has been designated in Israel recently as an unlawful association, for providing support and funnelling funds to Hamas, a terror group designated in the UK.
"Surely this must raise cause for concern for the public donating money for children, when one of the donors has been officially declared to be using that money to support a recognized terror group," it said.
In response, Islamic Relief Worldwide said it "categorically denies any links with Hamas".
It added: "Islamic Relief Worldwide is regulated in the UK by the Charity Commission and has rigorous internal control and compliance systems in place to ensure we uphold our humanitarian principles of impartiality, independence and neutrality."
About 2,000 people have died in Gaza since the fighting began last month.
Those killed include more than 1,900 Palestinians, mostly civilians, according to the United Nations. Sixty-four Israeli soldiers have been killed in the violence and three civilians in Israel have also died.
The DEC, an umbrella organisation which brings together 13 UK aid charities to deal with international crises, launched its campaign on 7 August. It said one and a half million people had "no or very limited" water or sanitation, with many in "urgent need of medical care".
The BBC and other public service broadcasters agreed to air a DEC Gaza appeal.
In 2009, the BBC and Sky chose not to broadcast a previous Gaza appeal, with the BBC's decision prompting angry protests and 40,000 complaints.
In a statement on the DEC's website on Thursday, addressing the "tone of the debate over Gaza", chief executive Saleh Saeed said: "The DEC's launch of a public appeal in response to the humanitarian crisis in Gaza has been wrongly interpreted in some quarters as a political statement.
"It is nothing of the sort. Giving aid is not taking sides."