Travellers and tourists have been struggling amid continuing large-scale strikes against the government’s plans to raise the retirement age from 62 to 64.
Only half of the country’s fleet of high-speed trains were running and regional trains, including in the Paris region, remain severely disrupted.
The French president called on striking workers to act “responsibly” and show “collective intelligence”.
Mr Macron said “things are getting better, some solutions have been found” to improve train services, and that the government was working “tirelessly”.
In Paris, eight of the 14 metro lines were closed and many others running sporadically.
In Paris’ Saint-Lazare train station, serving western France, Jean Baptiste Beudon was relieved to see his train was not cancelled.
He said: “We got confirmation two or three days before the departure, but we were still worried that we would not have our train.”
Aurelie Lecerf, travelling with her children, said: “We arrived here at six o’clock this morning to get a train. The last one was full but we should get the next one.”
Many people travelling for Christmas have sought alternative transport, using car-sharing services or bus companies – which have seen a surge in reservations.
Most transport unions have called for the strikes to continue during the holidays, as talks between the prime minister and union leaders over the last few days have failed to reach a compromise
Recent polls show a majority of French people still support the strikes over fears they will have to work longer in return for lower pensions.
However, a majority are also in favour of them being suspended during the festive period.
Hundreds of thousands have taken to the streets across the country in recent weeks. A general strike at the start of December saw police fire tear gas against violent protesters in Paris.
President Macron says the current pensions system is unfair and too costly.
It allows rail workers, mariners and Paris Opera House ballet dancers to retire up to a decade earlier than the average worker.
He wants a single, points-based system under which for each euro contributed, every pensioner has equal rights.