If you read the article you discover that any top secret label applied to the conversation was done so by the article's author, and Chirac apparently did not believe the conversation all that top secret else he would not have later confirmed the story in an interview.
I also see no benefit for the following people to collude in a common lie.
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In 2007, Dr. Romer recounted Bush’s strange behavior in Lausanne University’s review, Allez Savoir. A French-language Swiss newspaper, Le Matin Dimanche, printed a sarcastic account titled: “When President George W. Bush Saw the Prophesies of the Bible Coming to Pass.” France’s La Liberte likewise spoofed it under the headline “A Small Scoop on Bush, Chirac, God, Gog and Magog.” But other news media missed the amazing report.
Subsequently, ex-President Chirac confirmed the nutty event in a long interview with French journalist Jean-Claude Maurice, who tells the tale in his new book, Si Vous le Répétez, Je Démentirai (If You Repeat it, I Will Deny), released in March by the publisher Plon.
Perhaps those who think this story unbelievable have simply never spent much time with evangelicals - heck, Elliot Abrams of the Bush administration met with John Hagee to discuss foreign policy. It's hard to find a nutcase more outrageous than Hagee. He said Hurricane Katrina was God's punishment on New Orleans for its gay pride parade the week before. And he wants war with Iran to encourage the rapture and second coming.