Renault admitted last month it was hoaxed into wrongfully firing upstream development chief Michel Balthazard and two other executives after a company investigation incorrectly concluded they had received payments from Chinese companies via foreign accounts.
Renault security manager Dominique Gevrey, who had obtained more than 300,000 euros ($434,000) from the carmaker to pay an anonymous source for the information, was arrested on fraud charges after the espionage claims unraveled.
Renault fired the three executives in January on suspicion of industrial espionage, all of whom denied wrongdoing from the start. Renault last month apologized to the three falsely accused executives and offered to reinstate or compensate them.
Pelata offered his resignation at that time of the apology, but Renault CEO Carlos Ghosn refused to accept it, saying he did not want to add one crisis to another. Instead, Ghosn and Pelata pledged to forgo their 2010 bonuses and profits from 2011 stock options.
Earlier on Monday a Renault spokesman said a report by French TV channel iTele that Pelata's resignation had been accepted at a special board meeting on Monday was not correct.
Morgan Stanley analyst Stuart Pearson said Pelata's departure was a loss to Renault, although investors would not be surprised, and the fact that Carlos Ghosn was staying on as CEO would limit the impact on shares.
"Pelata as COO did a solid job of guiding Renault through the last few years," Pearson said, adding that his departure could hamper the new strategic plan Renault unveiled in February. "It does call into question the execution of the strategic plan that has only just been announced - Pelata would have been a key architect of that. It's not immediately obvious who could replace him."
Audit shows 'serious dysfunctions'
French Industry Minister Eric Besson said an external audit on the industrial espionage affair reveals "serious dysfunctions within the company's management."
Besson would not identify those responsible for the dysfunctions, adding that they were named in the audit report.