Just one high-speed TGV train out of seven will be running on average, and just one in five regional trains, the SNCF said, roughly on par with the cancellations seen on Tuesday.
For international services, traffic to Belgium on Thalys trains will be running almost as normal, while three out of four Eurostar journeys to London will be maintained and one in three to Germany will go ahead.
All trains to Switzerland and Italy have been cancelled.
In the Paris region, the main commuter RER trains will also be badly affected, with only one in three services scheduled on the popular B line, one in five on the C line and one in two on the A line.
Speaking to parliament, Prime Minister Edouard Philippe said the way the SNCF operated could not continue.
“I respect the strikers because going on strike is a constitutional right... But ... we also need to respect the millions of French who want to be able to get to work,” he said.
Transport Minister Elisabeth Borne urged unions to negotiate, but union leaders hit back.
“The railway workers are not doing this for the fun of it,” said Philippe Martinez, head of the hardline CGT union, the biggest among railway workers.
SNCF President Guillaume Pepy said the strike was likely to cost the company 20 million euros a day in lost revenue at a time when it is already adding three billion euros to its overall debt pile of 47 billion euros every year.
The four main rail unions plan to strike for two days out of every five for the next three months a total of 36 days of disruption to fight a shake-up of monopoly SNCF before it is opened to competition in line with European Union rules.
The protests come as France prepares to mark the 50th anniversary of the student-led riots of May 1968, when the entire economy came to a virtual halt. The work stoppages so far pale in comparison with those events.
The last French leader to square off against the rail unions came off worst. The strikes of 1995 paralyzed France and forced prime minister Alain Juppe to pull the measures a defeat from which he did not recover.
The unions are broadly weaker now and divided over how best to handle Macron’s many social and economic reforms a division Macron hopes to be able to exploit to his advantage.
If the 40-year-old president succeeds it will set the tone for other reform plans, including revamping the education system and overhauling pensions. Macron has already faced down the unions to ease labor laws, making it simpler to hire and fire.