The conservative group National Federation of French Muslims (FNMF), backed by Morocco, swept the voting for the French Council of the Muslim Faith (CFCM), taking 19 of the 43 seats in its administrative council, officials said.
That was three more than it won in the CFCM's first election in 2003.
The moderate Grand Mosque of Paris (GMP) group supported by Algeria advanced from six to 10 seats, ending up equal with the activist Union of French Islamic Organisations (UOIF) that slipped from the 13 seats it won two years ago.
The result was a setback for the UOIF, which has flirted with militant positions on issues such as the Muslim headscarf ban in state schools. Often described as fundamentalist by the French press, it has become increasingly moderate in the CFCM.
The strong showing by the Grand Mosque boosted the chances of its rector, outgoing CFCM president Dalil Boubakeur, to be re-elected to lead the religious council for France's 5 million Muslims, the largest Islamic minority in Europe.
"We think he has authority and reassures the French public," said one Muslim leader. The CFCM will elect its new head next Sunday and the heads of 25 regional councils in two weeks.
"These elections have given more legitimacy to the CFCM"
Abderrahim Berkaoui, spokesman for the FNMF party
The first-placed FNMF enjoys wide support among Muslims of Moroccan origin and from Morocco itself, but is not as organised as other groups.
The French government sponsored the launch of the CFCM in 2003 to create national and regional leaderships able to deal with state officials about problems Muslims face in the country.
The CFCM has given the country's 5 million Muslims a public voice they never had before, but rivalries between the UOIF and the Grand Mosque group have often blocked progress in tackling practical issues such as mosque construction or imam training.
"These elections have given more legitimacy to the CFCM," said FNMF spokesman Abderrahim Berkaoui. "Our apprenticeship is over. We now have three years to show what we can do."
Despite frequent criticism of the CFCM as ineffective, the campaign saw a surprising boom in the number of mosques joining in and hectic politicking within and among Muslim interest groups hoping to win influence in the councils.
About 1300 mosques took part this year, compared to 992 in 2003.
According to its statutes, the CFCM only deals with the religious aspects of Muslim life in France, such as the construction of mosques, training of imams and nomination of chaplains for hospitals, prisons and the military.
Only about 10% of French Muslims pray at mosques regularly, a fact secular Muslims cite to argue that the CFCM is not representative of all Muslims here.
But the mosque networks in the CFCM have become the de facto spokesmen for the minority.