The short-haul halt will mostly rule out air trips between Paris and regional hubs such as Nantes, Lyon and Bordeaux, with connecting flights unaffected.
Critics have noted that the cutoff point for comparable train journeys is shy of the roughly three hours it takes to travel from Paris to Mediterranean port city Marseille by high-speed rail.
The law does specify that train services on the same route must be frequent, timely and well-connected enough to meet the needs of passengers who would otherwise travel by air - and able to absorb the increase in passenger numbers.
People making such trips should be able to make outbound and return train journeys on the same day, having spent eight hours at their destination.
Although the measure was included in a 2021 climate law and already applied in practice, some airlines had asked the European Commission to investigate whether it was legal.
The government had already secured Air France's compliance with the plan in exchange for a 2020 coronavirus financial support package.
Competitors were banned from simply filling the gap.
Laurent Donceel, interim head of industry group Airlines for Europe (A4E), told AFP governments should support "real and significant solutions" to airline emissions, rather than "symbolic bans."
Brussels had found that "banning these trips will only have minimal effects" on CO2 output, he added.
Although the measure was included in a 2021 climate law and already applied in practice, some airlines had asked the European Commission to investigate whether it was legal.
A4E highlighted its own net zero by 2050 strategy, which includes switching to jet fuel from non-fossil sources and deploying battery- or hydrogen-powered aircraft.
The step comes as French politicians have also been debating how to reduce emissions from private jets.
While Green MPs have called for banning small private flights altogether, Transport Minister Clement Beaune last month trailed a higher climate charge for users from next year.
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