The top seed and defending champion whipped the world bronze medallist 21-10, 21-5 in 29 minutes in their semi-final at the Tokyo Metropolitan Gymnasium.
Lee will play the seventh seed and hometown favourite Kenichi Tago on Sunday, hoping to lift a record fourth Japan Open title.
Tago beat China's Gao Huan 21-12, 21-12 in the other semi-final.
On Thursday, Rashid Sidek tendered his resignation as Malaysia's national singles coach, according to press reports from Kuala Lumpur.
"Before I left Malaysia I was aware of various issues concerning the coaches," Lee said through an interpreter after his semi-final win.
"But I am an athlete and for now I want to concentrate on my game and win," said the 30-year-old, who was stretchered off with cramp and dehydration in the world championship final against his Chinese archrival Lin Dan last month.
Asked how he felt about the BAM, Lee said: "As an athlete, it may be impossible for me to change anything about the association.
