But the veteran coach says he never had any plans to quit the job just days before the Congolese play their first game at the tournament in South Africa.
Players refused to train on both Thursday and Friday in an attempt to get the Congo federation and government to pay over bonus money, which they have since been promised.
"This is crazy, it is devastatingly damaging to our preparations," Le Roy wrote on his blog.
"My players have been treated like children because the officials have not met their commitments to the players and to my staff. The players have refused to train in solidarity with those staff members who have not been paid," he explained.
"The players are very disappointed not to be taken seriously because they had been promised things that did not materialise.
"We need people to understand that footballers are no longer children. When they come to the Nations Cup they lose money that they would be getting in bonus payments at their clubs and they risk losing their place in the team. But they come because they are proud to wear this jersey," Le Roy wrote.
The team was now back in preparation for their opening Group B match against Ghana in Port Elizabeth on Sunday and Le Roy will take charge at a record-breaking seventh tournament.
"I never announced my resignation. I went to lock myself in my room. It is football that interests me. This is what keeps me going. Obviously, when you cannot train, I'm in morally abyss."