Correspondent Remy Pigaglio was put on a plane out of the country "for no reason", the newspaper's publication director Guillaume Goubert told AFP.
Pigaglio "was returning from holidays in France on Monday when he was detained by airport security," he said.
"After a night in the cells, he was expelled for no reason, although all his papers were in order," Goubert added.
"France deeply regrets this decision by the Egyptian authorities," said a foreign ministry statement.
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President Francois Hollande raised the question of media freedom during his visit to Egypt in April, the statement added.
Goubert said airport police had confiscated Pigaglio's passport and mobile phone and that it was hours before he was able to contact the French embassy.
"It appears that Egypt's intelligence service was behind the decision," he said.
In a statement published in La Croix, Pigaglio said no one had questioned him and he still did not know why he had been expelled.
Paris-based press freedom campaigners Reporters without Borders said it was "very disturbed" at the news and called for an explanation from the authorities.
Earlier this month, Egypt's journalism union accused the authorities of declaring war on media freedom.
In late April, Amnesty International criticised the authorities for a crackdown on anti-government activists.
President Abdel Fattah al-Sisi, who was elected in 2014, was feted by millions of Egyptians opposed to the rule of his predecessor, Mohamed Morsi, whom he toppled in 2013.
But he faces growing discontent over what critics call his heavy-handed rule.