Red yeast rice has been used in food, alcoholic drinks and folk medicine for centuries around East Asia.
The scandal erupted in March when the company, a household name in Japan, recalled three brands of dietary supplements after customers complained of kidney problems.
It later said it had detected a potentially toxic acid produced by the mould at one of its factories, and the government inspected the firm’s facilities.
Last month, the company said it was probing a total of 80 deaths possibly connected to its pills, and investigating whether organs other than kidneys were harmed.
But at the time the government called Kobayashi Pharmaceutical’s delay in reporting the number of cases under investigation “extremely regrettable”.
On Tuesday, the company’s board of directors said in a separate statement that they “pray for the souls of those who died … and offer condolences to the bereaved families”.
The company’s new president is Satoshi Yamane, previously head of sustainability policy, the company said.
Outgoing president Akihiro Kobayashi, who has expressed his intention to take responsibility for any harm caused, will remain in an executive role to manage compensation-related matters, it added.
Kobayashi’s red yeast rice supplements are regulated under a system created in 2015 under former premier Shinzo Abe.
Some watchdogs have reportedly expressed concerns that the regulation of these products is not sufficiently stringent and that they do not always have the advertised effects.
