The addition of Tokyo and Nagoya on Etihad's flying programme will bring to eight the number of destinations served by Etihad in the Far East, which currently includes Beijing, Jakarta, Manila, Singapore, Bangkok and Kuala Lumpur.
James Hogan, Etihad Airways chief executive officer, said: "Commercial and cultural ties between the UAE and Japan continue to grow and Etihad is proud to play a part in boosting these ties."
Total trade between the two countries currently stands at more than $40bn and Japan is the second largest foreign investor in the UAE with foreign direct investments of more than $4bn.
Current statistics indicate that 330 Japanese companies operate in the UAE and more than 3,500 Japanese nationals reside in the country and 8,800 in the Middle East region.
Nagoya is Japan's third-largest city and the fourth most populous urban area in Japan. It is home to the Suzuka track which hosts the Formula 1 Japanese Grand Prix.