L'Equipe quoted midfielder Alaixys Romao as saying the team had agreed unanimously to stay in the Angolan enclave of Cabinda for their first match against Ghana on Monday.
Rebels of the Cabindan separatist group FLEC sprayed the Togolese team bus with gunfire on Friday, killing the driver and wounding nine others. Two members of Togo's football delegation died on Saturday and one was undergoing surgery in South Africa.
A Togolese minister said on Saturday that the government had decided to pull the team out of the tournament, which starts on Sunday, because of "this dramatic situation".
But L'Equipe quoted Romao as saying: "We have just had a meeting of the whole delegation and we will be on the pitch on Monday to face Ghana."
Officials of the team and the Confederation of African Football, who organise the tournament, were not available for comment.
"The decision was taken unanimously," said Romao, who plays for French club side Grenoble.
However, English club Manchester City said on their website that striker Emmanuel Adebayor, Togo's captain, was returning home.
"People have died for the African Nations Cup, others have been injured. We can't let them down and leave like cowards," said Romao.
"If we stay here it's for them but also not to give any satisfaction to the rebels. Our government does not necessarily agree with us but we are all determined to play this competition."
