The Times newspaper reported that managing director Andy Street had made the critical comments at an event for entrepreneurs in London this week.
It said he described France as "sclerotic, hopeless and downbeat," and said "nothing works and worse, nobody cares about it."
Street also described the Gare du Nord station in Paris terminus for Eurostar trains from London as "the squalor pit of Europe" and told his audience: "If you've got investments in French businesses, get them out quickly."
"On reflection I clearly went too far," he said. "I regret the comments, and apologize unreservedly."
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The French embassy in London was unamused by the comments.
It told the Times that France had the world's fifth-largest economy, with world-class public services, a first-rate health care system and higher workforce productivity than many other developed countries.
John Lewis operates upmarket department stores in Britain.
It does not have any stores in France but is planning to launch a website for French customers.