Emmanuel Adebayor, the Togo captain, later told French radio RMC that the team would be returning heeding to the prime minister's call.
"We had a meeting between players yesterday [Saturday] and we told ourselves we were football players and decided to do something nice for our country by playing to pay tribute to those who died," Adebayor said.
"Unfortunately, the head of State and the country's authorities have made a different decision, so we will pack and go home."
The team's assistant coach and spokesman died of wounds sustained when the bus they were travelling in came under attack on Friday in Cabinda province, an oil-rich region separated from the rest of Angola by a thin strip of Democratic Republic of Congo.
An Angolan bus driver was killed at the scene.
'Determined to play'
Several players who survived the shooting earlier said that the team had decided that they would line up against Ghana in the first match of the tournament in tribute to the dead.
"People died for this tournament, others were injured. We can't abandon them and leave like cowards," Alaixys Romao, a Togo midfielder, was quoted as telling France's L'Equipe newspaper.
"Our government doesn't necessarily agree with us but we are determined to play in this competition. The decision was taken unanimously."
Thomas Dossevi, a Togolese striker who plays for the French side Nantes, echoed Ramo's remarks saying that the team would line up against Ghana for their first game of the tournament "in memory of the dead".
"We are all heartbroken, it is no longer a party, but we want to show our national colours, our values and that we are men," he said.
Witnesses said that the squad was seen training for Monday's scheduled game on Sunday morning.
Al Jazeera's Andy Richardson, reporting from Luanda, said: "The Togo team are tremendously proud of playing for their country.
"This is the premier tournament for football players on this continent, so if Togo do decide to stay it would not be a huge surprise."
'Attacks will continue'
The Africa Nations Cup is due to start in the capital Luanda with game between the hosts and Mali on Sunday. Seven matches of the three-week tournament were due to take place in Cabinda.
The Confederation of African Football (CAF), tournament organisers, said in a statement on Saturday that all the matches would go ahead as scheduled.
A group fighting for the independence of the oil-rich region, which is divided from the rest of Angola by Democratic Republic of Congo, claimed responsibility for the attack on Friday, saying it was aimed at the team's military escorts.
Rodrigues Mingas, the secretary-general of The Forces for the Liberation of the State of Cabinda-Military Position (Flec-PM) said the group would continue its attacks against Angolan targets.
"This attack wasn't against the Togolese it was against the Angolan occupation forces. We have nothing against Togo. We are supporting and admire their players a great deal," he told Al Jazeera from Luxembourg.
"We are not killers. Two months ago we wrote to the Confederation of African Football president, Issa Hayatou. On his desk he has our letters warning that there was a risk in organising the tournament in Cabinda.
"Cabinda is not Angola, we have no common border with Angola, our languages are different, we are from different tribes, we have nothing to do with them. They are occupying our country for the black gold."
Samuel Petrequin, a sports writer for The Associated Press news agency, told Al Jazeera that the streets of Cabinda were "peaceful" in the wake of the attack.
"It seems the games will go ahead as planned," he told Al Jazeera.
"There is no violence at all, maybe they can have the games as it was planned. The Angolan government said after the attack that it was going to increase security measures."
Al Jazeera's Mourad Labarab, reporting from Cabinda, said that security measures had become "very tight".
"The army have been deployed throughout the city and also we have seen checkpoints ... movement in the city has become very difficult and just getting close to the stadiums could take hours.