The hiring of family members by politicians has become a sensitive issue after conservative candidate Francois Fillon became embroiled in a similar scandal over parliamentary assistant jobs for his wife and two of his children.
Le Roux quit after financial prosecutors opened an inquiry into the allegations against him, although he insisted he did nothing wrong.
"Those work contracts ... correspond to work that was effectively carried out," said Le Roux in a televised statement, seeking to draw a distinction with the case of Fillon, who is accused of having paid his wife hundreds of thousands of euros for work she did not do.
Le Roux's quick resignation contrasts with Fillon's dogged refusal to step down as candidate even after magistrates opened a formal investigation into the allegations against him, a contrast his opponents could use to raise the pressure on him.
Even as he slipped from first to third in the opinion polls, meaning he could be eliminated from the May 7 runoff, Fillon quelled a revolt by some in his party who wanted him to step down in favor of a replacement candidate.
The inquiry into Le Roux was launched after Fillon allies suggested that any inaction by the judiciary in Le Roux's case would show that Fillon, who says he did nothing illegal, was the victim of bias by the judiciary.
The Quotidien TV show said on Monday that Le Roux had paid a combined total of 55,000 euros ($59,455) between 2009 and 2016 to his two daughters as parliamentary assistants during summer vacations, starting from when they were 15 and 16.
Le Roux, who just last Saturday directed the government's response to what prosecutors said was a thwarted attack at Paris Orly airport by a radicalized Muslim, will be replaced by junior foreign trade minister Matthias Fekl.
A source close to the Fillon investigation said the inquiry had been widened to include suspicion that false documents had been presented to justify employment.
Le Canard Enchaine, the newspaper which broke the allegations about the jobs for Fillon's relatives, reported in its latest edition that a Lebanese billionaire paid a company owned by Fillon $50,000 in 2015 to arrange introductions to Russian President Vladimir Putin and Total CEO Patrick Pouyanne.
There was no immediate comment from Fillon's campaign or Total. Fillon has consistently denied wrongdoing.