The polls yesterday were seen as a key test for the president whose Alliance for the Republic (APR) party is riven by divisions two years after winning a bitterly disputed election.
Early results published by local media showed that in Dakar the APR had been beaten by a coalition led by the outgoing mayor of the city, Khalifa Sall, from the Socialist Party (PS).
The PS, which led Senegal from 1960 to 2000, is part of the ruling coalition, but leaders failed to agree on shared party lists for the local elections.
The presidential party also appears to have been trounced in the cities and towns of Ziguinchor, Saint-Louis, Touba, Podor and Dagana, either by the opposition or by dissidents from within the ruling party, exit polls published by local press showed.
Many members of the government who were running in the local polls were beaten in their strongholds -- a blow for the APR who controlled only a few towns before the election and were hoping to reinforce their local support bases.
The local polls were a key test for Sall and his party, who had hoped the elections would allow the party to strengthen its base despite poor economic results and frustrations among the Senegalese that election promises have yet to be fulfilled.
More than 5.3 million people were eligible to vote for more than 2,700 councillors across the country.
Those councillors, from over 600 districts, will in turn elect mayors and heads of provinces. The official results are due to be announced by the end of next week.