PARIS (AP) _ Only about 50 long-distance trains ran throughout France on New Year's Day as rail workers continued their strike for a 15th day despite concessions from the state-owned railroad.

Two major unions said they opposed a railway management offer accepted by three smaller unions.

Rail services operating were about one-third of the normal schedule for Jan. 1, a public holiday thoughout the country, the railway management said. The southwest and the north were affected the most.

There were no trains whatsoever on the northern Paris suburban lines and one train in eight on other short-distance routes.

Government mediator Francois Lavondes announced after a meeting with unions and management that ended after midnight Wednesday that a proposal to base salary increases on merit rather than seniority would be withdrawn.

He said the current structure would remain in place until joint negotiations produced a new scheme based on ''a balance between merit and seniority.''

Lavondes said changes had been agreed upon in working conditions, particularly concerning rest days for travelling staff such as drivers and guards. They had surprised their unions by starting the strike as a wildcat action.

Only three small unions signed the agreement, however.

The communist-led General Confederation of Labor and socialist-led French Democratic Labor Federation said they did not accept the agreements.

Georges Lanque, secretary-general of the confederation's railroad division, said Thursday afternoon that all confederation branches which met to discuss the agreement voted to continue the strike.

The French Democratic Labor Federation said its members felt the management concessions were too limited to lead to a return to work. The feeling was strongest in major rail centers such as Paris-North, Lyon, Metz and Avignon, it said.

Non-confederation workers and remaining branches of the French Democratic Labor Federation were to vote Friday on continuation of the strike.

The railmen's strike coordination committee, a grassroots organization independent of the formal union structure, said Thursday that ''only continuation of the strike and its strengthening will make the (railroad) concede on all the demands.''