In a statement confirming Cho Yang-ho's resignation, the second change in less than two years at the helm of the local organising committee, Pyeongchang 2018 credited its outgoing president with getting preparations back on track and "managing critical issues" such as delayed venue construction, disputes over the location of the Olympic stadium and sponsorship.
Cho is chairman of the Hanjin Group, which controls Olympic sponsor Korean Air and a major shipping company struggling with heavy debt.
An official at South Korea's Ministry of Culture, Sports and Tourism said Cho's resignation had been accepted. The ministry official who didn't want to be named, citing office rules, declined to comment on how long it would take to appoint a new chief organiser for the 2018 Games.
Cho took over as president of Pyeongchang's organising committee in July 2014, succeeding Kim Jin-sun, the former governor of the region.
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"I can proudly say that POCOG has become a strong team, and the challenges we have overcome have allowed us to achieve success at our first official test events this past February."
Pyeongchang organisers have faced a series of challenges in recent years, including the construction delays, local conflicts over venues and criticism about their financial planning, but preparations had seemed to turn a corner after the successful hosting of test events earlier this year in Olympic snow venues.