Trade unions say they are open to negotiations and will stop striking at any moment if an agreement is found before June 28.
Rail service is expected to remain "very disturbed" Wednesday, with 86 percent of trains canceled nationwide, according to forecasts from state-owned SNCF.
Platforms at Gare du Nord, Paris's busiest railway station, were so crowded with commuters that some tumbled onto the tracks and had to be helped back up, television footage showed.
The "cheminot" status effectively guarantees jobs for life and other benefits, in keeping with the image of France's railways as an essential pillar of the country's infrastructure and its public services.
Mr Macron is planning to phase out SCNF's generous contracts, which include automatic annual pay rises, protection against dismissal, early retirement and free tickets for workers' family members. The railway sector is extremely sensitive in France, and when the government previously attempted reforms in 1995, the response was so poor that Prime Minister Alain Juppe eventually resigned.
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.
"This government has had an easy time so far, but this is a real political battle." former transport ministers Dominique Bussereau, who supports the government reforms, said on France2 television.
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".
"This reform is necessary for travelers, necessary for the SNCF, necessary for the railway workers", she told CNN's affiliate BFM TV on Tuesday. "The salaries aren't incredible, the work conditions are hard, and for some it means working every other weekend".
Air France workers also went on strike over pay today, although the company said it expected 75 per cent of flights to operate as usual. One in every three trains to Germany was to operate, while the Eurostar service connecting London, Paris and Brussels was down to three out of every four trains, the SNCF said.
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 protesting unions in France believe Macron's ideas would neither resolve SNCF's debt issue nor cure the railway's problems but would hurt the railways.
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. The rail disruptions have led to extremely heavy traffic jams on roads around Paris.
The Communist-rooted CGT wants the strike to spread beyond the rail sector.
Some energy sector workers walked out on Tuesday in protest against the planned liberalisation of the power sector, but there was little impact on power output.