Reports of Seki's departure also come more than two months after Nissan selected a new chief executive officer. Makoto Uchida took the role after Hiroto Saikawa resigned. Saikawa admitted that he and other Nissan executives were overpaid as part of a stock-related payment plan, though he denied any wrongdoing.

In its statement about Seki's resignation Wednesday, Nissan said that the automaker "has been on a steady path to regain trust, restore the company's performance and work on its business transformation, and is already seeing progress."

"Under the new top management, Nissan will continue to focus on these key areas, which remain our highest priority," the company said.

Bloomberg described Seki as one of the contenders to replace Saikawa before Uchida was tapped.

The Japanese news source Diamond Online quoted Seki as saying that he was not quitting because of troubles with the alliance.

"I would not say there is no confusion in the management," he told Diamond. "But it's not the reason I leave."

Seki told Reuters that Nidec, which produces specialist car parts, was an offer he could not refuse.

"I love Nissan and I feel bad about leaving the turnaround work unfinished," he told Reuters. "But I am 58 years old, and this is an offer I could not refuse. It's probably my last chance to lead a company, too."