The men’s team, which is already through to the quarterfinals, suffered a 1-4 defeat in their last group match, setting them up against Denmark in the last-eight stage on Friday.
Competing without top stars like Olympic medallist P V Sindhu and hampered by the injury-forced ouster of Saina Nehwal, the Indian women were outplayed by their Japanese opponents, who claimed the tie by establishing a 3-0 advantage.
Malvika Bansod was no match to world No. 5 Akane Yamaguchi as she lost 12-21 17-21 in the first match that lasted 34 minutes.
The pair of Tanisha Carsto and Rutaparna Panda then suffered an 8-21 10-21 defeat against the duo of Yuki Fukushima and Mayu Matsumoto as Japan took a 2-0 lead.
It was the same story for Aditi Bhatt as she was outplayed 16-21 7-21 in just 29 minutes in the second singles by Sayaka Takahashi as Japan sealed the best-of-five tie.
In the Thomas Cup match, only the doubles pair of Satwiksairaj Rankireddy and Chirag Shetty could manage a win in the men’s team championship tie as they beat He Ji Ting and Zhou Hao Dong 21-14 21-14 in a 41-minute contest.
The win by Rankireddy and Shetty duo boosted the confidence of the Indian team after a struggling Kidambi Srikanth began the day for India with a 12-21 16-21 loss to Shi Yu Qi in 36 minutes.
Sameer Verma gave a tough fight to Lu Guang Ju but eventually lost his singles match 21-14 9-21 22-24 after one hour and 23 minutes as India trailed 1-2.
The other doubles pair of M R Arjun and Dhruv Kapila went down fighting 24-26 19-21 to Liu Cheng and Wang Yi Lyu in 52 minutes before Kiran George lost to Li Shi Feng 15-21 17-21 in the 43-minute singles match.
The defeat against China was the first for the men’s team in the tournament.
It had beaten the Netherlands 5-0 on Sunday before notching up a victory against Tahiti by an identical margin on Tuesday to qualify for Thomas Cup quarterfinals for the first time since 2010.