Japan, which is a top travel destination for Hong Kong people, said it would limit flights from Hong Kong, Macau and mainland China to Tokyo's two airports, plus Osaka and Nagoya from Friday.
"It is understood that around 250 outbound flights of Hong Kong airlines will be affected between December 30, 2022 and the end of January 2023, affecting around 60,000 passengers," the government said in a statement late on Wednesday.
"We think that Hong Kong people should be allowed to use not just these four airports," Lee said.
Flights of Hong Kong airlines can still carry passengers back to Hong Kong from various airports in Japan, the government said, to "ensure the smooth return of Hong Kong people from Japan and to minimise the impact to Hong Kong travellers caused by the incident."
Hong Kong Airlines and Peach Aviation announced they would cancel some flight routes because of the rules.