Kim, 67, who had been President of the committee (POCOG) since 2011, had his resignation accepted by the government despite his term running until October 2015.
"Pyeongchang 2018 is at a turning point for the latter half of its Games preparation, which requires more detailed planning and execution," Kim said in a statement.
"At this critical juncture, I believe that Pyeongchang 2018 needs new leadership and a stronger system that will effectively carry out various Games-related projects. And this is why I decided to resign as President of POCOG."
Kim's departure follows that of Moon Dong-hoo, the Vice President and Secretary General of the committee, who tendered his resignation in May citing health problems but only quit earlier this month.
The organisation is in the process of a review by the Board of Audit and Inspection (BAI), who refused to say what prompted the investigation in the first place.
"Yes, there is an audit going on but it's not a regular audit. It is a specific-subject audit. POCOG is not big enough for us to audit regularly, like we do the ministry of culture, sports and tourism annually," a BAI official told Reuters.
"The process is still ongoing. We just completed only the on-site part of the months-long audit. Thus we have no result yet."
An official at the Ministry of Culture, Sports and Tourism denied that Kim's resignation was a result of the investigation and praised the outgoing president, who had been a special ambassador for Pyeongchang's successful bid after heading their two failed attempts in 2003 and 2007.
"He has made tremendous effort and substantial contribution to winning the bid and preparing for the Games," the official told Reuters.
"His resignation has nothing to do with the inspection from the BAI. Kim said since he has done building a foundation, such as stadiums, it makes more sense to bring in new talent to successfully host the 2018 Games. He felt that his role is done."
Local media said businessman Cho Yang-ho, head of the Korea Table Tennis Association, was the favourite to succeed Kim.
Cho, though, denied he would take up the role.
"Taking the position is a great honour for the country but I have a lot of work at hand that requires my full-time commitment," he said in a statement.
"Therefore I cannot take up the position as the head of POCOG. But I will do my best in order to make the 2018 Pyeongchang Winter Games successful."
(Writing by Patrick Johnston, editing by Nick Mulvenney)
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