Rachid Ghannouchi also reiterated a policy of his Ennahda party, which heads the country's new government, that Tunisia's Jews are "full citizens with equal rights and duties."
"Ennahda condemns these slogans which do not represent Islam's spirit or teachings, and considers those who raised them as a marginal group," Ghannouchi said in a statement.
Videos circulated online showed crowd members greeting Ismail Haniyeh, the prime minister of the Gaza government, at the airport in Tunis on Thursday chanting "Kill the Jews" and "Crush the Jews."
The chants came from Salafists, ultraconservative Muslims who have been making their presence felt in Tunisia recently.
After decades of being oppressed by Tunisia's secular dictators, Ennahda won elections and has been at pains to demonstrate its moderate credentials and belief in universal rights and freedoms to all Tunisians.
They have been repeatedly embarrassed by ultraconservative Islamic groups that have emerged since hard-line President Zine El Abidine Ben Ali was ousted from power last year in an uprising in Tunisia that led to revolts around the Arab world.
The groups have attacked university campuses and staged sit-ins over female students not being allowed to attend classes in the conservative face veils and have demonstrated over a variety of moral issues in cities.
'Death to Israel'
At a rally in a sports complex for Haniyeh on Sunday, supporters of the banned ultraconservative Hizb al-Tahrir party called for death to Israel, but did not repeat their anti-Jewish slogans.
For his part, Haniyeh told The Associated Press on Sunday night that he disagrees with the anti-Semitic slogans. "We are not against the Jews because they are Jews. Our problem is with those occupying the land of Palestine," he said. "There are Jews all over the world, but Hamas does not target them."
But Yigal Palmor, the spokesman for Israel's Foreign Ministry, said the chants revealed Haniyeh's true sentiments. "If he was greeted with anti-Semitic chants, then there must be a reason why his local friends thought this might please him," Palmor told the AP in Jerusalem.
Haniyeh is touring the Middle East to raise support for the militant Hamas group, which recently reconciled with its Palestinian rivals in the West Bank.
Tunisia's new government has tried to ease any fears the country's small Jewish community has over the nation's Islamist-tinged government.
The new president, former human rights activist Moncef Marzouki, went so far as to call on December 19 for any Tunisian Jews who had fled the country in the past to return.
Tunisia currently has a Jewish population of 1,500 Jews, but in the 1960s there were 100,000. Most left following the 1967 war between Israel and Arab countries, and Socialist economic policies adopted by the government in the late 1960s also drove many Jewish business owners out of the country.
Most now live on the resort island of Djerba, near the country's border with Libya.