The strike began at 6pm on Thursday and is set to last throughout the weekend.
An average of just six out of ten trains are running in the Rhône-Alpes region, though SNCF said in a statement that there were “notable disparities across geographical regions” in terms of service.
In the Loire, only 30 percent of trains are running whilst on the lines from Lyon to Chambéry, Annecy and Genevra, 70 percent will be running.
Suburban routes in Grenoble and Lyon have introduced extra stops on lines which are usually direct, increasing passengers' journey time.
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The strike is to protest 100 jobs being cut in 2016 and workers criticized SNCF for "accelerating the break-up of the company" after "a multitude" of structural changes which have had a "heavy impact" on railway workers and users.
In a letter on Thursday, the unions asked the national heads of SNCF to "take the matter in hand and to intervene with the local and regional directors to reopen negotiations very quickly" in order to avoid the strike.