Nick Clegg was asked on LBC about tweets by David Ward, Liberal Democrat MP for Bradford East, after the Paris terror attacks last week.
Mr Ward tweeted "Je suis Palestinian" as marchers gathered on Sunday following the attacks that left 17 people dead.
The MP said he was "disappointed" by his leader's comments.
More than three million people took part in Sunday's unity marches across France, with many displaying the slogan "Je suis Charlie" in a reference to Charlie Hebdo, the satirical magazine attacked by Islamist gunmen.
Mr Ward also tweeted that Israeli Prime Minister Benjamin Netanyahu's presence in Paris "makes me feel sick".
Mr Clegg said the Bradford MP "has repeated form on this" but he had not spoken to Mr Ward since the tweet.
The deputy prime minister told a caller to LBC "we are not suspending David Ward on this occasion" as his remarks, while offensive, were not as bad as comments he has made before which did lead to his suspension.
Speaking to the BBC, Mr Ward said he was "a bit disappointed" at Nick Clegg's criticism.
"Nick's got his own views and he is entitled to those views," he said.
"It's a contentious issue."
The MP denied his comments were aimed at Muslim voters in his constituency.
"I feel personally strongly on this particular issue," he said.
"Yes a lot of people in my constituency feel strongly about it who are Muslims.
"This is not a Muslim issue.
"Many, many people who applaud the stance that I take are not Muslims and I bitterly resent the accusation that what I'm doing and what I'm saying is somehow pandering to Muslims."
Mr Ward was suspended from the Lib Dem parliamentary party in July 2013 and had the whip withdrawn for three months over comments he made about Israel.
The suspension came after a long-running dispute with the party's leadership over his use of language and comments he made about "the Jews".
Last year he gave a "categorical apology" after tweeting: "The big question is - if I lived in #Gaza would I fire a rocket? - probably yes".
He later said his comments were not in support of firing rockets into Israel, and apologised if he had given that impression.
The deputy prime minister has called a tweet by one of his MPs "crass, stupid, offensive and highly insensitive".