FAS added that Lee has been an “integral part of the national team’s coaching staff, assisting coach Ogura in previous matches against China and the Korea Republic together with fellow assistant coach, Kosei Nakamura”.
Lee is also the head coach of Singapore Premier League side BG Tampines Rovers.
“The Football Association of Singapore extends well wishes to Coach Ogura and his fellow backroom staff member for a speedy recovery and expresses confidence in Coach Gavin Lee as he guides the Lions in their quest for victory against Thailand.”
Lee had been invited to join Ogura’s team for the March international window.
Ogura previously said that Lee’s expertise and understanding of the players at the club level were vital.
Singapore have one point from five matches in the qualifying group.
Singapore lost their first two matches in their qualifying group last November, falling 3-1 to Thailand and 5-0 to South Korea in the reverse fixture in Seoul.
In Ogura’s first match in charge, Singapore held China to a 2-2 draw, before losing 1-4 in the reverse fixture in Tianjin.
The team recently lost 7-0 against South Korea on Jun 6.