The countrys top teams, Hendra Setiawan/Mohammad Ahsan and Markis Kido/Marcys Fernaldi Gideon, were beaten by Chinese pair Fu Haifeng/Zhang Nan 21-17, 19-21, 11-21 and Lee Yong Dae/Yoo Yeon Seong from South Korea 10-21, 20-22.
"I felt I did not play well. I kept returning smash shots badly to allow my opponent to launch another attack," Hendra was quoted as saying by the public relations team of the All Indonesia Badminton Association.
Ahsan, meanwhile, expressed regret over his failure, along with Hendra, to defeat Fu/Zhang in the second set.
"Fu/Zhang had a good defense. They were not easy to defeat," he said.
The PBSI social media and public relations team said Hendra and Ahsan would immediately return to Jakarta to prepare themselves prior to the China Open Super Series Premier and Hong Kong Open Super Series 2014 in November.
The 2013 world champion will not take part in the French Open Super Series 2014.
The failure of Kido/Fernaldi, meanwhile, was reported to be caused by their own mistakes made in the second set when the score was 20-20.
"We regretted the failure in the second set very much. After equalizing the score through hard work we finally had to lose just because we were not calm. The Korean pairs defense was very strong to make it difficult to penetrate," Kido said.
In the mixed doubles event, two teams from Indonesia - Tontowi Ahmad/Liliyana Natsir and Riky Widianto/Richi Puspita Dili - will meet in the semi final round on Saturday local time.
The Denmark Open Super Series Premier is one of the most prestigious tournaments, offering a prize of US$600,000.
reporting by imam santoso