The aircraft landed at Haneda Airport at around 5.50 a.m public broadcaster NHK reported.
On board were the seven victims, their family members, as well as officials of companies where the deceased worked.
Three of those deceased were Makoto Okamura, 32, Yuko Sakai, 42 and Rui Shimodaira, 27, all of them employees of the Tokyo-based consulting firm Almec Corporation.
Other victims were Hideki Hashimoto, 65, Nobuhiro Kurosaki, 48 and Hiroshi Tanaka, 82, who were working for Oriental Consultants Global and Koyo Ogasawara, 56, an employee of Katahira and Engineers International.
Foreign Minister Fumio Kishida and Deputy Chief Cabinet Secretary Koichi Hagiuda were at the airport to offer flowers and a silent prayer.
Tamaoki Watanabe, who survived the attack with injuries, also returned. He was taken to a nearby hospital for treatment.
In total, 20 hostages (nine Italians, two Bangladeshis, one American, one Indian and seven Japanese) and two police officers lost their lives in the almost 12-hour terror siege on Holey Artisan Bakery, located in the Gulshan diplomatic area of Dhaka.