"Between late Wednesday and early Thursday, the national flags were all removed from the streets," an Asian Games organising committee spokesman told AFP.
The move followed protests by anti-North Korean activists about the appearance of the North Korean flag in the venue neighbourhoods.
"We decided to withdraw the North Korean national flag along with all the other national flags," the spokesman said.
The Yonhap news agency reported that the organisers were mainly concerned about the possibility of the North Korean flags being vandalised.
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The flags of participating nations had originally decorated streets near the main Games stadium at Incheon, outside the swimming and equestrian event venues and around a football stadium in Goyang city north of Seoul.
A Goyang municipal spokesman said conservative activists had peppered local officials with phone calls and texts protesting the flying of the North Korean flag.
North Korea is sending a 273-member delegation to the Asiad, which begins September 19. The first batch of athletes and officials was due to fly in to Incheon later Thursday.