MPs voted late on Saturday to some suspend some flights by domestic airlines that can be made by train in less than two-and-a-half hours, as part of a wider climate bill.
If the bill passes through France's upper house, the Senate, France will join a number of European countries seeking to move away from short flights.
But some have criticized President Emmanuel Macron for watering down proposals from his own environmental panel, which had recommended a ban on flights where a train journey would take less than four hours.
Transport Minister Jean-Baptiste Djebbari said the government's proposal was "reasonable." He told lawmakers during the debate that a four-hour threshold "would have really impacted territories that need flights."
"When there is a robust alternative, usually clients switch to trains," he said, citing routes from Strasbourg and Bordeaux to Paris. "Each time high-speed lines have competed with flights, we have noticed that trains have largely drained (airline passengers)."
Djebbari also said the bill would mean an end to flights from Paris' Orly Airport to Nantes and Lyon.
But the measures don't apply to routes that typically form part of a connecting international flight; meaning that the capital's Charles de Gaulle airport is largely spared by the move, because it is France's main international transport hub.
Left-wing MP Danièle Obono said the government's plan to move away from a four-hour limit would "save the three routes that emit the most greenhouse gas: Paris-Nice, Paris-Toulouse, (and) Paris-Marseille."
The four-hour proposal came from the Climate Convention citizens' panel, which was set up by Macron to take the temperature of the country on emission-cutting measures.
A number of European countries have sought to promote train travel as an alternative to domestic flights, even as the Covid-19 pandemic has put the airline industry under strain.
The €600 million ($714 million) government aid package for Austrian Airlines stipulated it cut its domestic flight emissions by 50% by 2050 and ended flights where a direct train alternative takes "considerably less than three hours."
In a similar move, the French government last year agreed on a €7 billion ($8.3 billion) rescue package for AirFrance that was tied to certain conditions, including "a drastic reduction of internal flights, limited to transfers towards hubs, whenever there is an alternative route by train that can be completed within two-and-a-half hours."