Vandals spray-painted the gravestones in the eastern town of Westhoffen, near Strasbourg, days after another incident in a nearby village.
In response, President Emmanuel Macron said France would fight anti-Semitism "until our dead can sleep in peace".
France is home to a Jewish community of about 550,000 - the biggest in Europe.
"Jews are and make France," Mr Macron said in a tweet on Tuesday evening.
"Those who attack them, even in their graves, are not worthy of the idea we have of France," he said.
France's north-eastern Alsace region, on the border with Germany, has been marked by a series of anti-Semitic acts in recent months.
Chief Rabbi Haïm Korsia said he was "outraged and horrified to learn of the desecration of yet another cemetery in Alsace".
As well as swastikas, the number 14 was used, a slogan linked to a white supremacist slogan.
The prefect of the Bas-Rhin region, Jean-Luc Marx, visited the site to express his support for the Jewish community.
The Westhoffen cemetery houses about 700 graves, including those of several relations of former Prime Minister Léon Blum, France's first Jewish leader before and shortly after World War Two.
Interior Minister Christophe Castaner, on a visit to the cemetery on Wednesday, said the attack was "an expression of pure hatred" and announced the creation of police taskforce against hate.
French Prime Minister Edouard Philippe expressed "revolt and disgust at the anti-Semitic inscriptions in two communes of Bas-Rhin", adding: "The perpetrators of these acts must be found and punished."
Last week, anti-Semitic tags were daubed on the walls of the town hall in Rohr, not far from Westhoffen. Jewish officials said one of the slogans in the attack on Rohr appeared to refer to the Jewish cemetery at Westhoffen.
Another town hall was attacked in the Bas-Rhin area in April, while in February, Nazi symbols and anti-Semitic slogans were spray-painted on more than 90 graves in the Alsace village of Quatzenheim.
One tombstone was defaced with the words "Elsässischen Schwarzen Wolfe" ("Black Alsatian Wolves"), the name of a militant far-right group active in the 1970s and 1980s.
France has seen a rise in anti-Semitic attacks in recent years, from Islamists as well as the far right.
On Tuesday night, France's National Assembly passed a draft resolution that includes hatred of Israel as an example of anti-Semitism.
The definition, by the International Holocaust Remembrance Alliance, has already been adopted by the European Parliament and several other countries.
A number of MPs from President Emmanuel Macron's ruling party voted against the resolution.
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