The top seed, runner-up last year, must beat in-form Boonsak Ponsana in the first round. The 11th-ranked Thai reached the final at the China Masters at the weekend, losing to home favourite Lin Dan.
Lee admitted he has been struggling with an unspecified knee problem he suffered before the China Masters.
“I still felt pains when I practised today but I prepared for the China Masters and Japan Open pretty well. I’m ready to do my best,” said Lee.
The winner of that match will take on either Hsieh Yu-hsing of Taiwan or Indonesia’s Simon Santoso before a probable third-round clash against defending champion Soni Dwi Kuncoro of Indonesia.
A strong-looking top half of the draw also includes Athens Olympic gold medallist Taufik Hidayat, also of Indonesia, and the 2008 Asian champion Park Sung-Hwan of South Korea.
“I took part in this tournament many times but I’ve never won, although I finished runner-up before. It’s the jinx I want to bury. So this is the tournament I really want to win,” said Hidayat.
The withdrawal of world number two Chen Jin of China leaves the bottom half wide open and boosts the chances of third seed Peter Gade of Denmark, who won the title in 1998 and 1999.
His main rivals are Tien Minh Nguyen of Vietnam, fellow Dane Joachim Persson and local hope Sho Sasaki.
“The Japan Open has always been one of my favourite tournaments. I don’t know how many Japan Opens I have left because of my age so I’d like to give my utmost best,” Gade said.
“I know it’s going to be difficult, there are a lot of good players like Chong Wei and Taufik. But I know if I play my best I still have a chance to win,” added Gade.
In the women’s competition, last year’s Super Series Masters Finals winner and top seed Zhou Mi of Hong Kong faces Adriyanti Firdasari of Indonesia in the first round.
China’s Wang Yihan, the in-form fourth seed who captured her first major title here last year and has won a clutch of titles this season, will be a threat to Zhou.
World number two Wang Lin is expected to face tough early tests against Asian champion Zhu Lin in the second round, and then possibly France’s Chinese-born Pi Hongyan.
The 2007 champion Tine Rasmussen of Denmark and India’s Saina Nehwal are also fancied.
Matches in the main draw start on Wednesday and the tournament runs until September 27.