Philippe has seen his popularity increase significantly in recent weeks.
Hidalgo is backed by the Europe Ecology-The Greens party, which gained strong influence nationwide.
France was holding the second round of municipal elections in 5,000 towns and cities on Sunday - one which were postponed because of the Coronavirus pandemic. Only 44.7 per cent of voters, a record low, cast ballots in the first round of the municipal elections. Her reelection will allow her to oversee the 2024 Summer Olympics.
Organisers also wore gloves and masks and in some places were kept apart from voters by plastic screens.More news: NY Reported Only 5 COVID-19 Deaths Saturday, Cuomo Says
The only region of France not voting Sunday was the overseas territory of Guiana in South America, where the pandemic was deemed too active to open polling stations.
A view of the documents, pens and bottles of hydroalcoholic gel before the second round of mayoral elections at the Hotel de Ville in Paris, France, June 28, 2020.
The first round of municipal elections was held two days before the government declared a lockdown on 17 March.
The spread of the coronavirus has slowed significantly in France in recent weeks and nearly all restrictions on social and business activity have been gradually lifted over the last month. France has reported almost 200,000 confirmed cases and 29,781 deaths in the pandemic.
Most restrictions have now been eased, but there is widespread anger at the government over shortages of personal protective equipment, including face masks, in the early stages of the pandemic.
The election is seen by many as a test of Macron's reforms and his handling of the outbreak.More news: Microsoft will close nearly all of its retail stores
"Although Macron has done a pretty good job of managing Covid-19, he has not been rewarded by his public", said Mr Mujtaba Rahman, Europe managing director for the Eurasia Group risk consultancy.
Prime Minister Edouard Philippe defeated a Communist challenger for the mayor's office in Le Havre with 58.83% of the vote.
A government reshuffle is expected to be carried out by Mr Macron in the wake of Sunday's result. The party, Republic on the Move, doesn't have candidates in every race and in some instances is backing candidates from both the left and the right instead.
Opinion polls now show Mr Macron's popularity rating is hovering around 40 per cent - higher than before the virus outbreak.
"There are places. where our own internal divisions brought us to results that were extremely disappointing", Ndiaye told French television.
The conservative Republicans party, which was the big victor in the 2014 municipal election, is expected to do well again based on its strong network of elected officials.More news: Iran issues arrest warrant for Trump over Qassem Soleimani killing
The anti-immigration, far-right National Rally, usually buoyed by low voter turnout in French elections, won a symbolic victory in the southern city of Perpignan, making Louis Aliot the first member of the party to run a city of more than 100,000 inhabitants since 1995.