Jean-Paul Delevoye became the target of unions' ire after admitting over the weekend that he had failed to disclose 13 private sector posts, both paid and unpaid, in a recent asset declaration.
One of his jobs, as president of the Parallaxe education think tank, paid nearly €5,400 ($6,000) a month on top of his ministerial salary -- money he should have forfeited under a 2013 political transparency law.
"Jean-Paul Delevoye made these omissions in good faith, he will now be able to explain himself," an official in the French presidency said, adding that Emmanuel Macron will name a new commissioner "as soon as possible".
Delevoye has said he will pay back the money, totalling more than 120,000 euros since September 2017.
But Laurent Berger, head of France's largest union, the CFDT, called Delevoye's omissions "shocking", telling France Info radio that "they obviously damage his credibility".
The unions are demanding that Macron drop his plan to forge a single pensions system out of the existing 42 schemes -- arguing that millions would have to delay their retirement to get full pension.
Macron has expressed his "solidarity" with the millions affected by the strikes but has so far shown no sign of backing down on what he has called "a historic reform".
Fresh demonstrations are planned for Tuesday, with several universities including the Sorbonne in Paris said they had cancelled or postponed year-end exams because students would not be able to show up.
A day of road blockades by truckers demanding higher pay added to traffic jams on Monday, which reached nearly 630 kilometres (390 miles) in Paris and its suburbs during the morning rush hour -- nearly double the average levels.
Most metro lines in the capital were again closed or operating just a handful of trains, and across France just one in three high-speed TGV trains and one in four regional trains were running.
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