South Korea, which is hosting the games, had asked the International Olympic Committee to decide whether the song's content was acceptable, but officials decided to make the cuts themselves while the IOC was still deliberating.
"We told the skaters to prepare for a version without the lyrics to avoid political controversy and to perform while we wait for the IOC’s decision," a spokesman for the Korea Skating Union said.
The IOC was not immediately available for comment
But, skaters Min Yura and Alexander Gamelin told reporters after a practice session on Wednesday that they had no problem with the change, as only a couple of words from the song would be omitted without any change to the music.
“Our concern was just not to step on any toes,” said Gamelin at the figure skating rink in Gangneung. “I think especially with unification, this whole theme is just coming together, peacefully.”
Japanese Prime Minister Shinzo Abe is scheduled to attend the Games opening ceremony in the city of Pyeongchang on Friday, when delegations from North and South Korea will march together under a single flag, and their athletes will compete as a single team in some sports.
The two Korea's efforts to achieve a thaw in relations have introduced a new dynamic to the region's complicated diplomacy.
While South Korea and Japan have worked together with the United States to try to persuade the North to abandon its nuclear and missile programmes, the two Koreas both harbour bad memories of Japan's occupation of the peninsula from 1910-1945.
Japan has already complained to South Korea about fans waving a Korean peninsula flag at a friendly women's ice hockey match on Sunday between the combined North and South Korean team and Sweden.
The flag depicted a map of the undivided Korean peninsula, including the disputed islands -- known as Dokdo in Korean and Takeshima in Japanese - located in the Sea of Japan, known to Koreans as the East Sea.
In response to that complaint, South Korea's unification ministry said that the joint Korean team would only use a version of the unified flag, approved by the IOC, which does not show the disputed islands.
This latest diplomatic irritant comes during an awkward phase in relations, as South Korea's government has criticised a 2015 agreement that a previous administration struck with Japan for an apology and compensation for former "comfort women" forced to work in Japan's wartime military brothels. [nL4N1PJ06Y]
Sensitivities over the islands could have potentially flared again during the ice dance competition as these Olympics will be the first Winter Olympics to feature figure skaters performing to music with lyrics.
The South Korean ice skaters will dance to the song "Arirang Alone", performed by Korean singer Sohyang.
The song's reference to the islands is contained in the final line of the verse;
"Far into the East Sea lies a lonely island
A strong wind will be blowing today again
As you are facing the wind with your small face
Dokdo, last night did you sleep well?"
A Korea Skating Union spokesman said the words "Dokdo, last night" will be erased.
During the London Olympics in 2012, the IOC prohibited the Korean footballer from the bronze medal ceremony for showing a sign which read "Dokdo is our territory," after South Korea's victory, although he received his medal later.
(Reporting By Jane Chung and Elaine Lies; Additional reporting by Soyoung Kim, Karolos Grohmann and Linda Sieg in TOKYO; Editing by Amlan Chakraborty & Simon Cameron-Moore)
