In the Paris region only two Metro automated trains with no drivers were fully running as the other 14 metro lines remained closed or only very partially running.
Most regional and national trains were at a standstill while international train routes also suffered disruptions.
Lorry drivers launched a separate protest on Monday, staging road blockages across France to demand better salaries and working conditions.
Mr Macron said last week he wants the government to “continue the work” on the pension changes, which include raising the retirement age to 64 and ending special privileges for some workers.
Major unions want to push the strike through Christmas as a new round of protests across France was planned for Tuesday.
The strikes involve mostly public sector workers, including train drivers, teachers and hospital employees, who fear they will have to work longer for lower pensions.