The law came into force two years after lawmakers had voted to end routes where the same journey could be made by train in under two-and-a-half hours.
The ban all but rules out air travel between Paris and cities including Nantes, Lyon and Bordeaux, while connecting flights are unaffected.
Critics have described the latest measures as "symbolic bans".
Laurent Donceel, interim head of industry group Airlines for Europe (A4E), told the AFP news agency that "banning these trips will only have minimal effects" on CO2 output.
He added that governments should instead support "real and significant solutions" to the issue.
Airlines around the world have been severely hit by the coronavirus pandemic, with website Flightradar24 reporting that the number of flights last year was down almost 42% from 2019.
The French government had faced calls to introduce even stricter rules.
France's Citizens' Convention on Climate, which was created by President Emmanuel Macron in 2019 and included 150 members of the public, had proposed scrapping plane journeys where train journeys of under four hours existed.