A spokesman said her resignation was not related to the accounting issue.
The Osaka company said in February it was under investigation by Japan's Securities and Exchange Surveillance Commission for possible earnings misstatements.
It said in March and repeated Monday it might restate its earnings for four years through March 2004, following reports it may have failed to account for more than $1.57 billion in losses.
The company is also dealing with several recalls of its lithium-ion batteries used in cell phones and laptop personal computers.
Nonaka, 52, a former TV journalist, took the chief executive and chairwoman post in 2005, becoming the first woman to head a major Japanese electronics company.
She ran Sanyo along with President Toshimasa Iue, grandson of the company's founder, who started Sanyo in 1947 making bicycle lamps.
Sanyo seeks to turn around its struggling business by trimming jobs, reducing factory space and dropping business lines under a 2004 restructuring plan.
The company posted a 31 percent operating-profit increase in 2006's October-December quarter over a year earlier.