The company said late on Tuesday that Chief Executive Markus Jooste had resigned with immediate effect after the discovery of new information prompted the company's supervisory board to ask consultants PwC to perform an "independent investigation".
"The Supervisory Board of Steinhoff wishes to advise shareholders that new information has come to light today which relates to accounting irregularities requiring further investigation," it said in a statement.
The furniture retailer postponed its results announcement and a webcast scheduled for Wednesday until further notice.
Jooste had been at the helm of Steinhoff for nearly 20 years and oversaw its expansion from a furniture manufacturer in South Africa to one of the largest household goods retailers in the world.
Billionaire Christo Wiese, Steinhoff's largest shareholder and chairman, will take over in an executive capacity on an interim basis.
Steinhoff, which has its primary listing in Frankfurt, said Wiese would "embark on a detailed review of all aspects of the company's business with a view to maximising shareholder value".