During a meeting with the country's Grand Rabbi Haim Bittan, President Moncef Marzouki said that Tunisia's Jews are full citizens and those that had left were welcome to return.
His comments come almost two weeks after Israeli deputy Prime Minister Silvan Shalom called on the country's remaining Jews to emigrate to Israel.
Tunisia presently has a Jewish population of 1,500, 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.
Marzouki, a veteran human rights activist, struggled for years to highlight the plight of the oppressed in the country under dictator Zine El Abidine Ben Ali.
Tunisians overthrew their dictator in January. In an October 25 election, a long-repressed Islamist party took the most votes and formed a new government with two left wing parties.
The rise of Islamists prompted Shalom – during a December 6 memorial ceremony for Tunisian Jews who died in the Holocaust – to call on Tunisia's Jews to flee the country for the safety of Israel.
The Islamist Ennahda Party has stated that Jews in Tunisia are full citizens with full rights. A number of prominent Jews in the country have rejected Shalom's call.