Yoshio Sekine, vice-chairman of the Japan Badminton Association, confirmed on Tuesday that the players from China had pulled out of the tournament.
"Chinese athletes cancelled their appearance in this tournament, which is unfortunate," he said at a Japan Open news conference, without discussing the motives for their withdrawal.
"However, there are still a lot of good athletes in this tournament and I am sure they will put on a good performance."
Another official at the event said that while he had not heard any specific reason for their absence "some sort of political reason could be suspected".
A long-standing dispute over an uninhabited group of islands in the East China Sea -- known as the Senkaku in Japan and Diaoyu in China -- took a fresh twist on Tuesday after two Japanese activists landed on one of the islands.
Beijing described the landing as provocative, lodged a complaint with Tokyo and said it reserved the right to "take further action".
As anti-Japan protests flared across China, cycling's governing body (UCI) expressed concern for Japanese riders taking part in races there.
"What matters is everyone's safety and it is true that the situation can become worrying," the UCI's Global Cycling Promotion director Alain Rumpf told Reuters.
"For the moment, we are being told that the Japanese interests in China can be threatened".
A UCI official told Reuters that Japanese team Aisan had been kicked out of the Tour of China and that there were fears a similar move could be made at the Oct. 9-13 Tour of Beijing.
"It is true that Japanese were expelled," UCI President Pat McQuaid told Reuters.
It was unclear whether a Japanese rider from a Malaysian team had also been kicked out.
Li Yongbo, the general coach of China's badminton team, was reported as saying the cancellation was due to the team's tiredness after playing at the Olympics, the Badminton Super League and the Masters Super Series in a row.
Li could not be reached by a Reuters reporter.
An employee of the Table Tennis & Badminton Management Center at General Administration of Sport of China said the decision to miss the tournament in Japan had been made in the past two days, but she would not say why.
The political row escalated on the anniversary of Japan's pre-war invasion of its giant neighbour, with relations between Asia's two biggest economies deteriorating badly.
The dispute led to a day of anti-Japan protests in China.
Japanese businesses shut hundreds of stores and plants across China and Japan's embassy in Beijing again came under siege by protesters hurling water bottles, waving Chinese flags, and chanting anti-Japan slogans, evoking war-time enmity.
Last week the Japanese government decided to nationalise some of the islands, buying them from a private Japanese owner, in a move which inflamed the dispute.
Political analysts say China also upped the stakes last week when it announced precise boundaries for waters it claims around the islands.
China's badminton elite would appear to be another casualty of the diplomatic row.
Brief profiles of the leading Chinese players still appeared on the tournament's website on Tuesday in a section highlighting favourites for victory.
Japanese player Sho Sasaki was disappointed the Chinese would not be taking part.
"Honestly speaking, I enjoy playing against opponents from China," he said. "It is one of the things I look forward to, and without their presence in this tournament, there is something that seems lacking."
Their absence opens the door for Malaysia's world number two Lee Chong Wei to reclaim the title, having suffered a shock defeat to China's Chen Long in last year's title match.
"It's unfortunate that China have withdrawn as it will certainly dilute the level of competition," Malaysia's singles coach Rashid Sidek said. "Chong Wei is our trump card."
With the Chinese out of the men's draw, Lee Chong Wei is seeded first seed, Denmark's Peter Gade second, Simon Santoso of Indonesia third and Japan's Sho seeded fourth.
The women's draw is headed by Dane Tine Baun, South Korea's Ji Hyun-sung, Ratchanok Intanon of Thailand, and South Korean Yeon Ju-bae.