The opening of a judicial probe is the first step toward a trial, but falls just short of an indictment.
If found guilty on charges of contesting the truth of historical crimes against humanity, Garaudy faces up to a one-year imprisonment and a $60,000 fine.
Pierre Guillaume, the director of Vielle Taupe, which published Garaudy's book, also has been targeted for possible charges.
Garaudy, who was expelled from the French Communist Party in 1970, was born a Protestant, but later converted to Catholicism. In 1982, he converted to Islam.
Garaudy chose as his lawyer Jacques Verges, who once defended Lyon Gestapo Chief Klaus Barbie and international terrorist Carlos the Jackal.
The controversy over Garaudy's book erupted after a Roman Catholic priest who helped Jews flee Nazi-occupied France defended Garaudy as an "honest man."
Abbe Pierre, 83, who has spent his life helping the poor and who tops opinion polls as France's best-loved public figure, praised Garaudy for questioning the accuracy of the 6 million figure.
Pierre also said it was excessive to term the book historical revisionism.
Pierre's support of Garaudy, a longtime friend, shocked his followers and dismayed members of human rights groups.The Catholic Bishops' Conference also rebuked Pierre for backing Garaudy's book, deploring his attitude and distancing itself from his statements.
"We reject the extremely serious confusion and scandal that have resulted from the support" Pierre has given Garaudy, the conference said in a statement. "The extermination took place. It's a proven fact. It was genocide. The gas chambers existed."
The chief rabbi of France, Joseph Sitruk, and Jean Kahn, president of the Consistoire, the official body representing French Jewry, applauded the church's position.
Monsignor Jacques Gaillot, a human rights activist whom the Vatican fired last year for his liberal views on birth control and AIDS, urged Pierre to retract his support for Garaudy.
"It's not possible to be on the side of the poor and support negationism at the same time," Gaillot said.
Meanwhile, the mainstream anti-racist organization MRAP is seeking to take Garaudy to court on the additional charge of inciting racial hatred, which is punishable under French law by up to five years in jail.
And the International League Against Racism and Anti-Semitism, known as LICRA, summoned Pierre, who has been an honorary member of the group for 20 years, to provide them with an explanation.
During his meeting with LICRA, Pierre sought to distance himself from Garaudy, stressing his "visceral" distate for Holocaust denial.
But some of his statements seemed certain to generate further controversy.
Pierre told LICRA officials that he had "no doubt that the concentration camps existed."
But, he added, "it seems that there may have been some excesses in generalizing that gas chambers operated in all the camps."