The CGT union said it counted 2.3 million protesters across France, including 550,000 in the capital. The turnout was massively higher than May Day last year but smaller than the biggest protests seen against the pension reform this year.
In the capital, radical protesters threw projectiles at police and broke windows of businesses such as banks and estate agents, with security forces responding with tear gas and water cannon, AFP correspondents said.
One policeman, hit by a Molotov cocktail, has suffered severe burns to the hand and to the face, Paris police told AFP. The police said 46 people have been arrested in the capital alone so far.
French Prime Minister Elisabeth Borne on Monday slammed as "unacceptable" violence that erupted in several cities during May Day protests venting anger at her government's pension reform.
"In many cities in France, this May Day was a moment for responsible mobilisation and commitment. The scenes of violence on the sidelines of the demonstrations are all the more unacceptable," she wrote on Twitter.
The main May Day march in Paris kicked off at 1200 GMT along the traditional protest route of Place de la Republique to Place de la Nation, with a heavy downpour suddenly beginning at the very moment it started.
Monday marked the first time since 2009 that all eight of France's main unions have joined in calling for protests.
Unions had been hoping for a vast turnout across France for the May 1 protests to further rattle Macron, who has been greeted by pot-bashing and jeers as he toured the country seeking to defend the reforms and relaunch his second mandate.
"This workers' holiday will take place amid union unity and that alone is historic," said Frederic Souillot, the secretary general of the Force Ouvriere (Worker's Force) union.
Radical ecological activists from Extinction Rebellion earlier sprayed orange paint on the facade of the glitzy Foundation Louis Vuitton museum in Paris, which is backed by the LVMH luxury goods giant.
In a separate action by a different environmental protest group, activists sprayed orange paint around the Place Vendome in central Paris, known for its jewelry shops, targeting the facade of the Ministry of Justice.
Police had been given a last-minute go-ahead to use drones as a security measure after a Paris court rejected a petition from rights groups for them not to be used.
Macron last month signed a law to raise the retirement age from 62 to 64, despite months of strikes against the bill.
Macron and his government have tried to turn the page, hoping to relaunch his second term after the reform was signed into law.
"The page is not going to be turned as long as there is no withdrawal of this pension reform. The determination to win is intact," said CGT chief Sophie Binet at the Paris protest.
"The law has been passed but has not been accepted, there is a desire to show discontent peacefully to have a reaction in response that shows a certain level of decency," said Celine Bertoni, 37, an academic in the central city of Clermont-Ferrand.
"I still hope that we are going to be told it will be withdrawn," she added.
"The mobilization is still very, very strong," added Laurent Berger, head of the CFDT union.
"It is a sign that resentment and anger are not diminishing."
Police used tear gas in Toulouse in southern France as tensions erupted during the demonstrations, while a car was set on fire in the southeastern city of Lyon.
In the western city of Nantes, police also fired tear gas after protesters hurled projectiles, AFP correspondents said. The windows of Uniqlo clothing store were smashed.
"Macron has the impression that as he was elected he has all the power! But I want him to cede his place to the people," added Karine Catteau, 45, in the western city of Rennes.
France has been rocked by a dozen days of nationwide strikes and protests against Macron and his pension changes since mid-January, some of which have turned violent.
When Macron attended the final of the French football cup on Saturday, he was met with activists waving red cards.
Almost three in four French people were unhappy with Macron, a survey by the IFOP polling group found last month.
PM Borne, with Macron's support, invoked in March the controversial article 49.3 of the constitution to ram the pension reform through parliament without a vote in the hung lower house.
Borne last week pledged to cut unemployment and make industry greener as she sought to move on to other affairs of state.
She also postponed any discussion on a controversial immigration bill until the autumn for lack of a parliamentary majority, saying she believed it was not the time for another divisive debate.
Labor unions early last month walked out of talks with Borne after she refused to budge on the pension reform's headline measure of raising the retirement age.