Courtois played in Saturday's 1-1 home draw with Austria in Euro 2024 qualifiers but told Tedesco after the match he would not make himself available for Tuesday's game against Estonia.
Tedesco said Courtois was unhappy that striker Romelu Lukaku was given the captain's armband for the Austria game in the absence of injured regular skipper Kevin De Bruyne.
However, the 31-year-old Real Madrid keeper disputed that account and hit back at Tedesco.
"I want to make it clear that it is not the first time or the last time that I talk to a coach about issues related to a locker room, but it is the first time that someone decides to tell it publicly," he said in a statement.
"I am deeply disappointed with this, but I want to make it clear that the coach's assessments do not fit with reality."
Courtois said he had never demanded anything from Tedesco and that he had already spoken to Lukaku to clear things up.
The keeper, who has 102 caps since making his national team debut in 2011, said he made himself unavailable after undergoing a check-up for a problem with his right knee.
"The medical team of my club and the national team were in contact and reviewed all the corresponding material to make the decision to leave the training camp," he added.
His father, Thierry, also told Belgian media he had pulled out of the Estonia game with a knee injury but Tedesco dismissed this.
"I wish I could say it's an injury but I can't lie," said Tedesco, who described Courtois as the "best goalkeeper in the world". "I always try to protect players but that's impossible in this situation."
Belgium have four points from their opening two qualifiers in Group F, having also won 3-0 in Sweden.
