The carrier announced the flight adjustments on Thursday amid growing concerns about a long-feared megaquake predicted to hit Japan.
The airline said affected passengers could rebook for other destinations, including other cities in Japan and mainland China, as well as Taipei, Bangkok and Da Nang in Vietnam.
It added that those who choose to refund their tickets would receive compensation in the form of travel vouchers.
“We deeply apologise for the inconvenience caused by this flight adjustment and promise to do our best to assist affected passengers and provide proper travel arrangements,” it said.
Kagoshima and Kumamoto are both popular tourist destinations. The former is often compared with its Italian sister city, Naples, with a mild climate, palm tree-lined streets and rumbling Mount Sakurajima, while the latter is famous for Kumamoto Castle, which is one of the country’s largest and most complete.