Chirac condemned the torching of the mosques which occurred early on Friday, assuring the Muslim community of his sympathy and support.
Prime Minister Jean-Pierre Raffarin expressed indignation at the incidents in eastern France and said he had ordered "that everything be done to find the perpetrators of these outrages".
But Muslim leaders were up in arms, criticising the political establishment for failing to attend a silent demonstration at Annecy, where one of the attacks occurred.
One fire devastated an 80-square metre prayer room in nearby Seynod, while the other seriously damaged the heating system at the mosque in Annecy.
"No leading political figure came," Kamel Kabtane, a local Muslim community leader, told demonstrators massed outside Annecy mosque.
"We are in a pre-electoral period and many politicians did not dare come, fearing perhaps a backlash from voters," he added.
There were no public indications Saturday who was behind the attacks.
Chirac phoned Dalil Boubakeur, head of the pro-government French Council for the Muslim Religion (CFCM), and Kamal Kabtane to express his utter condemnation of what he described as odious acts, a presidential statement said.
It said Chirac "expresses his sympathy and support to all the Muslims of France and assures them of the government's determination to find and punish those who carried out these attacks".
Chirac (C) sent apology to Paris
mosque head Dalil Boubakeur (L)
In a letter to Kabtane, head of the mosque in Lyon, Raffarin said: "I will personally ensure that you will be kept informed of the progress of investigations into these unacceptable acts."
"I wish it to be understood that I firmly condemn all attempts by those who try to propagate hate in our country," the prime minister went on.
Meanwhile, the CFCM described the attacks as "unspeakable, racist and anti-Islamic" and Boubakeur warned such acts "can only worsen the sensitive religious climate in our country."
The CFCM is the first recognised national council for the country's estimated five million Muslims.
France is home to an estimated
five million Muslims
The Representative Council of Jewish institutions in France also strongly condemned the attacks, expressed full solidarity with the Muslim community and demanded "a forceful response from authorities".
Muslim leaders had called for mosques to benefit from the same level of protection as synagogues.
French Justice Minister Dominique Perben on Friday said the perpetrators, being sought by police, should be given exemplary punishments.
Perben said he wanted a tough new law against racially and religiously motivated attacks, passed last year to be applied. The law provides for jail terms for offenders of up to 20 years.