The winners of the encounter, which will take place at Istora Gelora Bung Karno on August 19, should face defending Asian Games champions South Korea, who will take on Thailand, in the quarter-finals.
"I see our road to the final as very difficult, but from the beginning we already knew we were not favourites," national men's head coach Misbun Sidek told Astro Arena.
"However, I am optimistic for our young players to show their best performances."
The draw held on Thursday also saw Thomas Cup winners China, hosts Indonesia and Chinese Taipei receive byes to progress straight to the quarter-finals.
Are You ready for ASIAN GAMES 2018!
— Badminton Asia (@Badminton_Asia) August 16, 2018
Here is the anticipated draw results for Badminton
Women's and Men's Team Draw!!! @asiangames2018 pic.twitter.com/gCtD25l3nq
The Japanese side should be led by newly crowned world champion Kento Momota, while Malaysia will be without Lee Chong Wei, who is still recovering from his illness.
The Malaysia men's team, who won bronze in South Korea four years, consists of Liew Daren, Lee Zii Jia, Leong Jun Hao, Soong Joo Ven, Tan Wee Kiong, Goh V Shem, Teo Ee Yi, Ong Yew Sin, Chan Peng Soon, and Goh Soon Huat.
Meanwhile, Malaysia will not be involved in the women's team competition this year.