CEO Markus Jooste resigned with immediate effect after the discovery of new information that has prompted the German-listed company's supervisory, or non-executive, board to ask consultants PwC to perform an "independent investigation".
Steinhoff doubled down on Africa when it bought discount clothing retailer Pepkor in 2015 for about $5.7 billion at the time.
Shares in South Africa-based German-listed retail giant Steinhoff fell nearly 60% on Wednesday after the company announced the resignation of its CEO in the wake of alleged accounting irregularities.
The JSE says it's been talking to Steinhoff to find out the exact allegations against the worldwide company after the furniture retailer shares plummeted.
Chairperson of Steinhoff Holdings International, Christo Wiese will step in as interim CEO after Jooste's resignation.
It will also "determine whether any prior years' financial statements will need to be restated", its statement said.
In its statement the company added: "Shareholders and other investors in Steinhoff are advised to exercise caution when dealing in the securities of the group".
Steinhoff has been aggressively expanding in developed markets since moving its primary share listing from Johannesburg to Frankfurt in 2015, snapping up Britain's Poundland, US-based Mattress Firm and Australia's Fantastic.
"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 JSE's director of issuer regulation John Burke told Reuters the bourse was in talks with Steinhoff to get answers on the investigation of possible accounting irregularities.
Jooste, who had been with Steinhoff since 1988 and was CEO of Steinhoff International since 2000, was credited with growing the South African furniture manufacturer and retailer into Europe's second-largest player, behind Ikea, via a string of acquisitions including France's Conforama chain.
It is unclear what accounting irregularities the company was referring to in its statement on Tuesday.