Sakito has been credited with leading a successful marketing push for the iPod in Japan.
According to the Associated Press, Sakito resigned Monday after he reached reached an agreement Apple, though details of the agreement are unclear.
However, the Nihon Keizai Shimbun, Japan's top business daily, reported in its Tuesday's editions that Sakito plans to start setting up a venture business.
The report said that Apple's Japan operations will have a major change in its leadership at a time when competition in music players may heat up as rivals, such as Sony Corp., plan a big push in portable players.
As Apple searches for a successor, Phil Schiller, the company's Senior Vice President of Worldwide Marketing, will oversee Sakito's role in an interim position, according to the AP.
Sakito was said to be "the most visible executive" in the iPod's Japan push, and the Nikkei said his departure highlights divisions with the managerial ranks.