Amid persistent fears of coronavirus contagion, just over a third of voters had turned out by 5:00 pm, three hours before polling stations close, the interior ministry said.
The turnout rate of 34.67 percent was lower even than nine hours into the first round of voting on March 15 that was marked by a record 55-percent abstention rate.
Three polling agencies predicted participation would reach no more than 41 percent by the day's close, compared to 62.2 percent in 2014.
Polls opened for some 16.5 million eligible voters at 8:00 am (0600 GMT) in nearly 5,000 cities and towns where the first election round failed to yield a decisive outcome.
This represents about 15 percent of the country's municipal councils where power remains up for grabs, including the key cities of Paris, Lyon, Toulouse, and Strasbourg.
The opening election round was held just as the COVID-19 pandemic was gaining deadly momentum, but the second phase, originally scheduled for March 22, was postponed after France went into lockdown.
A new date was set after the government's scientific council said it was possible to hold another round safely, but voters were required to wear face masks and urged to bring their own pens to lower the contamination risk.
Many voters and election officials sported germ-blocking plastic visors, and plexiglass screens were erected between them at several polling stations, which also provided sanitising hand gel.
“If one can go shopping, why not go vote?” said an undeterred Martine Legros, 67, who cast her ballot in Dijon in eastern France.
Analysts expect the election to confirm that Macron's centrist Republic on the Move (LREM) party — founded by the president ahead of his 2017 election win — has failed to gain a strong foothold at local level.
The party made lacklustre showings in March — notably in Paris where Macron's candidate, former health minister Agnes Buzyn, came third.
“The problem is that the LREM is a new party that has no local roots and is struggling to impose itself as a (political) force,” analyst Jean Garrigues of the University of Orleans told AFP.
With a death toll approaching 30,000, France has been badly hit by the COVID-19 pandemic.
The country went into lockdown on March 17, just two days after the first round of municipal voting.
Most restrictions have now been eased.
During the outbreak, Prime Minister Edouard Philippe — an unshowy technocrat — saw his popularity rise to a level higher than that of Macron, whose policies have been the target of months of protests and strikes.
Macron's critics say he is a president of the rich and out of touch with ordinary people.
Paris is buzzing with speculation that a poor showing by the LREM on Sunday could see Macron reshuffle his cabinet, possibly axing Philippe who campaigned to be mayor of the Normandy port city of Le Havre.
Holding two executive posts is allowed under French law.
Firing Philippe would allow Macron “to claim he is delivering on his promise to ensure the 'second act' of his presidency takes note of failings revealed by his handling of the COVID-19 crisis,” said Mujtaba Rahman of the Eurasia Group risk consultancy.
With just 22 months to the next presidential election, Macron's main challenger is far-right leader Marine Le Pen of the National Rally.
Despite an abysmal performance in the last national elections, France's Socialists are expected Sunday to keep key regional centres, including Paris.
There will also be close attention on the Europe Ecology – The Greens party, which has its eye on the Alpine hub of Grenoble as well as Strasbourg and Lyon.
In Marseille, leftist Michele Rubirola hopes to take France's second city from the right after a quarter of a century of control.
For Le Pen's National Rally, the big prize would be Perpignan in the south, which could become the stage for the first far-right takeover of a French city of more than 100,000 inhabitants since 1995.
The only region of France not voting Sunday is the overseas territory of Guiana in South America, where the pandemic is deemed too active to open polling stations.