Polls show Le Pen and Macron among four leading candidates with a chance of coming out on top of Sunday's first round and reaching the May 7 runoff, in an unpredictable vote seen as a bellwether for global populist sentiment.
Macron and conservative candidate Francois Fillon have pledged more robust counterterrorism efforts, but remain committed to Europe's open borders.
The men, born in 1993 and 1987, of French nationality, had the intention of committing an attack on French soil within the next few days, he said.
The pair, who police said were seized in the southern port city a few moments apart from each other, were radicalised French nationals aged 24 and 30, the minister, Matthias Fekl, said.
A definite attack had been headed off, he said. The arrests come five days before the French go to the polls in the most uncertain French presidential election in the country's recent history - nearly a third of the electorate is still undecided and the four front-runners are clustered around 20 percent in the polls for the first ballot. A search of a rented apartment was continuing. Sources close to the investigation said at least two assault weapons had been found.
"The main candidates were warned in the middle of the last week that there was a risk and that two individuals had been identified". We received their photos and security of the candidates.
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France remains in a state of emergency and on high alert over possible terrorist attacks.
In a reference to Le Pen, Macron said voters had the choice of "hope and courage over resignation".
"Everything has been put in place to ensure the security of this big event for our democracy and our Republic. The security forces are mobilised everywhere across France to ensure the security of French people and to ensure the presidential campaign goes smoothly", he said.
Security has already been a strong campaign theme, and far-right candidate Marine Le Pen hardened her tone Tuesday on foreign extremists and border controls while centrist Emmanuel Macron called for national unity and stronger intelligence.
Search warrants seen by Reuters described the two men as risky.
The source told Reuters that that the men appeared to have turned to radical Islam during a term in prison.
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