French-based Chedjou and Nounkeu from Galatasaray both arrived with injuries and have been ruled out of the Group I match after being examined by Cameroon's medical staff.
Tottenham defender Assou-Ekotto was absent for "family reasons", the coach said.
"Missing these players means the match will not be easy for us although we'll be playing at home," said Norwich City defender Sebastien Bassong, who could stand in.
"Togo has some very good players, notably their key striker Emmanuel Adebayor. I watched them perform very well at the recent African Nations Cup in South Africa, so we must put in extra effort to win the match."
Cameroon are third in Group I on three points, two above Togo who have yet to win a game.