A senior SNCF manager, Alain Krakovitch, told Le Parisien that only 12% of high-speed TGV trains would operate on Tuesday, and the low-priced Ouigo service would be at a standstill.
Public support for the rail strike stands at just below half, according to an Ifop poll released Sunday, and commuters expressed a mixture of sympathy and frustration with the reduced service.
Taking on the railway company's 74,000 workers will be tough for Macron, after he pushed through a liberalization of France's labour code and cut taxes on capital in his first year in office.
At the Gare de Lyon station in eastern Paris, platforms were so packed that commuters spilled over onto the tracks as they waited for infrequent trains.
Worldwide train services also face disruption: no trains were set to run between France, Switzerland, Italy and Spain.
SNCF manager Guillaume Pepy, mentioned: "I have to be really clear ... the strike activity will definitely be thoroughly complied with as well as his mosting likely to make the lives of many various other individuals really challenging".
It will be a major test of the French trade unions' clout.
Union protests against Macron's earlier measures were timid and quickly faded.
As the industrial action began, almost one in two SNCF staff stayed off work.
Train movements to other countries like the UK, Belgium, Spain, Switzerland and Italy will also be affected because of the strike - from partial to total.
Travelers are livid as simply one in 8 high-speed TGVs are arranged as well as simply one in 5 local trains, leaving travelers on jampacked trains.
What remains unclear is whether Macron might offer further concessions to get the unions to back down before the strikes bite.
Macron eyed the reforms to make France more competitive and his plans were being compared with former United Kingdom prime minister Margaret Thatcher's showdown with the coal unions of Britain in the 1980s.
Macron wants to transform SNCF, which adds $3.69 billion (3 billion euros) of debt a year to a pile now running at $57.80 billion (47 billion euros), into a profit-maker.
The Macron government wants to phase out the special SNCF contracts, proposing to put new hires on contracts like those that apply elsewhere in industry.
The unions say the debt was caused by excessive investment in TGV trains at the expense of everyday connections and accuse Macron of paving the way for privatisation.
Borne has sought to ease tensions with assurances that current SNCF employees that have to move to a competitor in the future would keep most of their advantages.
- One in every three trains to Germany was to operate and three-quarters of Eurostar trains to London and Brussels will run.
Meanwhile, France is set to be hit by even more strikes on Tuesday, with garbage collectors, some energy sector staff, and Air France employees walking off from their jobs. The railway strikes are set to continue till June 28. Further walkouts are planned at the airline for April 7, 10 and 11.
Pensioners, students and public sector workers have also taken to the streets in recent weeks protesting against far-reaching reforms by Macron, who insists he was elected on a mandate for change.