While there was no damage at the new building site, the temporary mosque was gutted, firemen at the scene said early on Saturday.
According to the mayor's office, between 4000 and 5000 Muslims are estimated to live in Aubagne which has a total population of 43,000. There have never been tensions in the community before.
"For the time being we have no leads on the perpetrators or the motivation for such an act," said a police spokesman.
"We are moderate people and we have no room for fanatics," Bin Yunus Khaldi, a spokesman for Aubagne's Muslim community, said.
France, which is home to Europe's largest Muslim and Jewish
communities, has seen an increase in attacks on both communities in the past few years.
While many blame young, disaffected members of France's Muslim community for attacks on Jews, some believe nationalist extremist groups are responsible for targeting both communities.
In recent weeks, Jews have been arrested in connection with attacks on Jewish community centres.