The first direct commercial flight from Japan to Cuba arrived at Havana's Jose Marti International Airport on Tuesday evening.
Japan Airlines is planning three more chartered flights to the communist country this month under an agreement reached in March, with more slated in the coming months, JAL officials said.
But there are no plans to operate regular flights between the two countries, they added.
The Boeing 747 jumbo jet with 279 passengers aboard took off from Kansai International Airport in Osaka on Tuesday afternoon.
The direct flight took about 17 hours. Travel to Cuba usually takes nearly double that as passengers must stop over, usually in Mexico.
JAL's four chartered flights were set up at Cuba's request. The country has been actively promoting tourism in recent years, particularly targeting Japanese tourists in a bid to obtain more foreign currency and promote bilateral relations with Tokyo, the JAL officials said.
About 5,000 of the 1.7 million tourists who visited Cuba last year were Japanese.
The JAL officials claim Cuban music and cinema is growing in popularity in Japan and therefore they expect the number of Japanese tourists visiting the island to grow.