Zipair Tokyo is replacing the logo that appears on the tails of its airliners. The design is based on the letter "Z," which has Russian-military connotations.
The low-cost carrier will gradually replace the design from Saturday.
Company officials say they took into account the fact the letter "Z" often appears on the Russian military's vehicles used in the Ukraine conflict.
Japan Airlines established Zipair four years ago. It flies five routes. Three connect Narita airport outside Tokyo to destinations in Asia. The rest go to the United States. The carrier is scheduled to launch a service to San Jose, in the US state of California, in December.