More than £9 million was raised by the Disasters Emergency Committee (DEC) drive in its first week, partly thanks to full-page promotions in a number of newspapers.
But the appearance in the Chronicle of the ad - which featured a picture of a young Palestinian boy and said thousands more were "injured, homeless and living in fear" - sparked anger from some readers.
The quantity of complaints received and anger expressed online was sufficient for the newspaper to issue a statement saying: "We apologise for the upset caused". Including the ad was "meant as a purely humanitarian gesture" and was "not an expression of the JC's views", it said.
A large majority of the comments posted to the online statement were critical of the decision to apologise.