President Jair Bolsonaro suffered big losses in Brazil's just-completed municipal elections, with only five mayoral candidates he supported winning their races and none of them in the most important cities.

The president's worst rebuff came in his hometown of Rio de Janeiro, where Mayor Marcelo Crivella was battered in a runoff election Sunday, losing to his center-right predecessor, Eduardo Paes, by 64 per cent to 36 per cent. Crivella, an evangelical pastor, repeatedly used the president in his campaign to try to turn his fortunes.

Another big defeat for Bolsonaro came in Fortaleza, Brazil's fifth most populous city, where little known center-left candidate Sarto Nogueira topped Wagner Gomes, the president's favorite, 51.5 per cent to 48.5 per cent. Gomes had led opinion polls before the campaign began and often displayed Bolsonaro's support, but he sought to distance himself in the campaign's waning days.

A Bolsonaro candidate also lost in Belem, one of the capitals of the Amazon, though it was a close vote. Leftist Edmilson Rodrigues edged Everaldo Iguchi and will be the city's mayor for a third time.

Sao Paulo, a metropolis of more than 12 million people that is Brazil's biggest city, gave just 10 per cent of its vote to Bolsonaro's candidate, Celso Russomanno, who finished fourth.

Sunday's runoff was between two critics of the president, and resulted in center-right Mayor Bruno Covas easily winning reelection over socialist Guilherme Boulos by 60% to 40%.