Arsenal midfielder Song was expected to play a key part in the Indomitable Lions' bid to qualify from Group E but looks set to be employed off the bench initially on Monday.
Regular goalkeeper Carlos Kameni could also be another surprise exclusion, with Le Guen revealing in a press conference today he was set to select 36-year-old Hamidou Souleymanou between the posts.
"We've had three weeks of hard training and I've had a better idea of my team now," Le Guen said.
"Alexandre Song may not start the first match against Japan.
"This does not mean there is anything bad about him. He is a great player. I try to pick the most competitive team."
Le Guen pinpointed the speed of Japan's attacking players as the key area of concern.
"I have watched many videos of Japanese football over and over and I know their strongest weapon is that they have very swift attackers," he said.
"We've worked very hard to deal with that and as concerns Monday's match, I'm full of confidence."