"Korea is ready to welcome the world. We will welcome all eligible athletes and National Olympic Committees (NOCs), including DPR Korea," he said at a meeting of the Association of National Olympic Committees (ANOC) in the Czech capital.
The nuclear-armed northern neighbour has been a constant source of concern ahead of the Pyeongchang Games, which will take place from February 9 to 25 just 80 kilometres (50 miles) from the heavily fortified Demilitarized Zone which divides the Korean peninsula.
Countries including France and Australia contemplated staying at home after North Korea carried out its sixth nuclear test in September -- by far its most powerful yet.
But Lee insisted the Pyeongchang Games would be an "Olympics of peace and harmony."
"Safety is the (organising committee's) primary concern," he said, adding South Korea had hosted an NOC security workshop last week.
"The Korean government has also organised a special taskforce to ensure the coordination of all Games security," added Lee.
Lee added that all buildings and infrastructure for the Games were ready, while the high-speed KTX rail from Incheon to Pyeongchang would open in December.
"The construction of direct highways from Incheon to Pyongchang has also been completed," said Lee.
Addressing concerns about empty stadiums, also fuelled by the North Korean threat, Lee said the organising committee was "committed to ensuring full stadia," without elaborating.
Over the two weeks of the Games, 1.18 million tickets are available, with 180,000 sold internationally so far.
But South Korea is far from the traditional winter sports markets of Europe and North America, making domestic sales crucial, and South Koreans have bought little more than 160,000.
"Yes, we are worried about the ticket sales," ANOC Secretary General Gunilla Lindberg told reporters in Prague.
"We are working together with the Pyeonghang organisers and with embassies all over the world to get the promotion of the games."
"Some of the venues are sold out, like figure skating and short track. Cross-country skiing is not a big sport in South Korea," Lindberg added.