The leaders criticised the political establishment for failing to attend a silent protest demonstration at Annecy on Saturday, where one of the attacks occurred.
One fire totally 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 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.
The French Council for the Muslim Religion (CFCM) described Friday's attacks as "unspeakable, racist and anti-Islamic".
Its leader, Dalil Boubakeur, warned that such acts "can only worsen the sensitive religious climate in our country".
"No leading political figure came (to the demonstration)... We are in a pre-electoral period and many politicians did not dare come, fearing perhaps a backlash from voters"
Muslim community leader
There were no public indications on Saturday as to who was behind the attacks.
But President Jacques Chirac has assured the Muslim community of his sympathy and support.
He said the government is determined "to find and punish those who carried out these attacks".
And in a letter to Kamel Kabtane, Prime Minister Jean-Pierre Raffarin said: "I wish it to be understood that I firmly condemn all attempts by those who try to propagate hate in our country."
Muslim leaders have called for mosques to benefit from the same level of protection as synagogues.
French Justice Minister Dominique Perben has said he wants a tough new law against racially and religiously motivated attacks passed last year to be applied to the perpetrators.
The law provides for jail terms for offenders of up to 20 years.