Francois Hollande, in a speech to welcome the new king of Spain on his first official visit to Paris, said Europe's economic crisis had sparked both a spirit of defiance against the EU - and regional breakaway movements.
The Socialist leader, who is struggling in the polls, said he believed in "cohesion over division" in remarks that were immediately interpreted in Madrid as an allusion to Scotland and Catalonia, both of which plan independence referendums this autumn.
President Hollande told Felipe VI, who replaced his father Juan Carlos I in June, that he had come to the throne at "an important time for the EU".
Mr Hollande continued: "The crisis has hit hard, and that creates a defiance with regard to the European Union. Feelings of alienation nurture the temptation to withdraw and regional identities, which tomorrow will want to become national identities.
"Today millions of young people in France and in Spain are living through the brutality of unemployment, so we have only one obligation: that all these talents don't go to waste.
"That's why we work together to re-direct EU towards growth, employment, youth; so we create a spirit of solidarity and cohesion over division and fear."
Traditionally centrist France has several regions with embryonic demands for autonomy, including the island of Corsica. It also has ongoing concerns about the Catalan and Basque lands of Spain.
The Iberian press quickly picked up the president's remarks. "Hollande warns of regional entities that wants to become national ones," headlined El Periodico in the Catalan capital of Barcelona last night, before adding: "The president of France alludes to Scotland and Catalonia without naming them."
Mr Hollande, meanwhile, is also trying to fight off a challenge from France's answer to UKIP: the fiercely Eurosceptic and anti-immigration National Front won this year's European elections.
Sources in Paris have suggested the French have long-term strategic and military concerns over Scottish independence. This has not, however, translated in to any open intervention and few expect France to try and block Scottish EU membership.
Conservative politician Joelle Garriaud-Maylam, in a report to French Senate on Scotland and the EU earlier this year, said: "It seems reasonable to think most member states will align their position with London, which has already signalled it would respect the results of the referendum."
However, the Elysee has made no public comment on Scottish independence. A spokesman for Better Together was careful not to claim that Mr Hollande had. However, he said: "Across Europe there is a debate between those who believe we will be more prosperous and secure by working together and those who prefer to blame others and divide people.
"This is an important and timely warning from the French President."
SNP MSP Christian Allard said: "An independent Scotland will be a positive member of the EU and international community. With a Yes vote in September, Scotland will finally be able to speak with our own voice at the EU top table.
"The Westminster system is gearing up to rip us out of the EU as the No parties dance to UKIP's tune. Last week's promotion of Philip Hammond to UK Foreign Secretary has put one hand on the exit door. Leaving the EU would put Scottish jobs under threat - it is a risk we cannot take."