Atlaoui's execution would "not be without consequences on our bilateral relations", ambassador Corrine Breuzé told a press conference on Friday.
France, which abolished the death penalty in 1981, is "opposed to it everywhere and in any circumstances", she said.
Atlaoui, a welder, was arrested at the ecstasy laboratory but claims he thought it was an acrylics factory. Eight other people were arrested with him.
"What seems shocking to us is that our compatriot is the only one on the list of people who could be executed today," Breuzé said, adding that he had no contact with the drugs.
Atlaoui has appealed to Indonesia's Supreme Court.
Atlaoui's wife, Sabine, made an emotional appeal to Indonesian President Joko Widodo at the press conference.
"My husband is not a drug baron," she declared. "He does not deserve the death penalty. Listen to your soul and conscience, don't execute my husband."
Joko has promised to crack down on drugs and six people, five of them foreigners, were executed by firing squad in January, causing Brazil and the Netherlands withdrew their ambassadors in protest.
Atlaoui is among several others now facing a probable death sentence.