The North Korean Olympics ferry sailed past sanctions temporarily into Mukho port in the South's eastern city of Donghae, an hour's drive from the main Olympics venue in Pyeongchang.
A North Korean ferry arrived in South Korea on Tuesday carrying a 140-strong orchestra to perform at the Winter Olympics this week, taking advantage of a rare sanctions exemption from Seoul 16 years after its previous visit.
Protesters waved South Korean flags, torn up drawings of North Korean leader Kim Jong-un and blasted loud music from loudspeakers as the cruise ship pulled into a South Korean port. They also burned a paper version of the North Korean flag.
The protesters appeared to number only a few dozen or so. They were contained by hundreds of police as the Mangyongbong 92 cruise ship arrived in Donghae, about 120 kilometres (75 miles) east of Pyeongchang.
Some crew members were visible on the deck of the ship, flying the North Korean flag, as it prepared to dock in the south for the first time since 2002.
Seoul's Unification Ministry said the ferry, the Mangyongbong 92, would be escorted into the eastern South Korean port of Mukho at 17:00 pm KST (0800 GMT).
The ministry said it had decided to temporarily lift a ban on North Korean ships to "support a successful hosting of the Olympics", which begin on Friday. It is also a fresh sign of a thaw in inter-Korean relations after months of tensions over North Korea's nuclear and missile programmes.
Seoul banned all North Korean ships entering its ports and cut off most inter-Korean exchanges, including tourism, trade and aid, in 2010 in the wake of a torpedo attack by the North on a South Korean navy warship that killed 46 sailors.
The art troupe from the North is led by star singer Hyun Song Wol and is scheduled to perform at Gangneung, near the Games venue of Pyeongchang, on Thursday and in Seoul on Sunday.
It will use the vessel for transportation and lodging, the Unification Ministry said.
The ship last crossed into South Korean waters when it carried a North Korean cheer squad for the 2002 Asian Games in the port city of Busan.
Karaoke, ice cream and smuggled parts
Named after a mountain peak, the Mangyongbong 92 was given by a group of pro-Pyongyang Korean residents in Japan in 1992 to Kim Il Sung, the North's national founder and grandfather of current leader Kim Jong-un, to celebrate his 80th birthday, according to the Unification Ministry.
It features dozens of cabins of different classes, including special rooms where Kim Jong-un's father and grandfather stayed, as well as a restaurant, a bar equipped with a karaoke machine, and a shop where guests can buy souvenirs and snacks, such as ice cream, video footage and images from the 2002 show.
It can carry 350 passengers, Seoul officials said.
The ethnic Koreans who donated the ferry had used it to travel between Japan and North Korea, sending money and other resources back to North.
However, Japan barred the ship from its waters in 2006 in response to a long-range missile test by the North, resulting in a sharp fall in trade, remittances and other exchanges.
The ferry has also been suspected by Japan and others of being used to smuggle parts for Pyongyang's illicit nuclear and missile programmes.
North Korea's state media has rejected the smuggling accusations as a plot to "justify the hostile policy" of the United States and its allies.
"The conservative media and persons claimed that the use of 'Mangyongbong-92' ... during the Olympic period falls foul of the 'independent sanctions' by the US and South Korea," the official KCNA news agency said last month, when the two Koreas were holding talks on the North's participation in the Games.
"This represents the unpleasant and uneasy mind of the US and the South Korean conservative forces displeased with the trend for the improvement of the north-south relations created after entering the new year," it said.
Pyeongchang ready to battle cold snap, norovirus
The Pyeongchang Winter Olympics are on track though organisers are battling the spread of a virus among staff and preparing to deal with the cold snap at Friday's opening ceremony, Games chief Lee Hee-beom said on Tuesday.
"We are fully operational with many of our athletes and officials here and settling into their life in the villages and training is underway at all venues," Lee told a news conference.
But he said some 1,200 private security staff have been sidelined as fear of a norovirus among some of them has forced organisers to replace them with military personnel pending medical tests.