Assistant coach Sebastien Migne said Le Roy had written his letter in the heat of the moment and discussions on whether he would stay with the team were taking place.
Congo Football Federation president Constant Omari headed to Port Elizabeth on Friday to deal with the strike, 48 hours before the team's opening match at the tournament.
Before leaving Johannesburg, Omari said all was fine in the camp but players have now gone two days without training as they seek to force payment of promised bonuses.
Players had also staged a mini strike during last weekend's training camp in the Middle East.
Most players had already received payment but several of the team's coaching staff had been left out and the strike was in solidarity with them, officials said.
"We have had nothing but problems throughout the build-up," Migne told reporters on Friday. "We feel a little abandoned by the Congo government over the issue of bonuses and allowances."
Squabbling over bonus payments and allowances is a time-honoured tradition at the Nations Cup, usually a three-way tussle between players, their football association and government, who bankroll the campaign.
Frenchman Le Roy, 64, is a towering figure in the African game and will extend his record of tournament appearances to 29 games if he takes charge of the Congolese side in their opening Group B match against Ghana in Port Elizabeth on Sunday. He was a Nations Cup winner with Cameroon in 1988.
