The armed front for the Liberation of the Enclave of Cabinda (FLEC) have claimed responsibility for the attack, which has cast doubts over whether the tournament will go ahead.
Souleymane Habuba, CAF's communications director, insisted that while his sympathies lied with the Togolese national side, the tournament would take place as planned.
"Our great concern is for the players, that's our key priority, but the championship goes ahead," he said.
"We need to know all the facts about what's happening on the ground, we haven't got them all yet. We can't give a full reaction from reports that we have got from the media."
Habuba went on to question why Togo, in contrast to the other 15 teams making their way to Angola for the tournament, had elected to travel by road rather than flying.
"CAF's regulations are quite clear, teams are required to travel by air, not road," he continued.
"We had a meeting of all the teams this morning, or at least almost all of them - Togo didn't show up, and it was only later on Friday afternoon that we heard via information from the media that they had been the victims of an attack.
"But at no point were we told they were travelling by road."
However, Premier League clubs are preparing to bring their players back to England after the horrific ordeal, which came two days before the start of the tournament in Angola.
Manchester City - whose star striker Emmanuel Adebayor was not harmed in the attack in Cabinda - and Portsmouth have contacted the Football Association, asking them to speak to football's world governing body to ensure players' safety can be guaranteed, and calling for them to be sent home if it cannot.
A spokesman for Portsmouth, who have a number of players away on African Nations Cup duty, said: "We will be asking the FA to talk to FIFA to ensure the players' safety. That is paramount, and if the players' safety can't be ensured, then the players should be sent home."
The team bus came under an attack that, according to reports, left the driver dead and six other passengers injured, including two of the Togo squad. Romanian club Vaslui confirmed their defender Serge Akakpo was one of the players who had been shot and badly injured in the attack.
Manchester City released a statement relating to Adebayor, which read: "Manchester City can confirm that striker Emmanuel Adebayor is uninjured after this afternoon's attack on the Togo team bus in Angola.
"Club officials have spoken with Adebayor and, though shaken by the terrible events, he is unharmed.
"The club would like to send its condolences to the family of the driver and sends best wishes for a speedy recovery to the injured.
"We are currently in talks with the Football Association over what may happen next."
Aston Villa have also confirmed their midfielder Moustapha Salifou is "shaken but okay" following the attack after managing to make contact with the 26-year-old's brother.
Villa boss Martin O'Neill told his club's official website: "I am really shocked to hear about this.
"Obviously I am pleased and relieved to hear that Moustapha is okay and that he is not among the injured people.
"The club have been in contact with him and he has reassured us that he is okay but he is extremely shocked and upset, which he would be in these circumstances."
The Confederation of African Football and FIFA are yet to confirm the details of the attack or what effect it may have on the format of the tournament, or indeed whether it can go ahead at all.
Romanian side FC Vaslui confirmed Akakpo, who joined the club from French side Auxerre last year, was shot and badly injured in the attack.
The club said, though, the 22-year-old was out of danger after being treated by doctors.
A statement on the club's website read: "Badly injured in an ambush in Angola, Serge Akakpo is now out of danger.
"Akakpo was struck by two bullets in the attack and has lost much blood.
"His condition was stabilised by doctors.
"FC Vaslui have been in touch with relatives of the player, who confirmed he has undergone surgery, which went very well."
Togo and Nantes striker Thomas Dossevi told French radio station RMC: "I'm okay but several players are in a bad state.
"We are still at hospital. We were machine-gunned like dogs and had to remain hidden under our seats for around 20 minutes to avoid the bullets."
Midfielder Alaixys Romao admits the players feared the worst and thinks Togo are now likely to pull out of the tournament.
"We're not thinking yet of what could happen," said Romao, who plays his club football for Grenoble.
"But it's true that no-one wants to play. We're not capable of it.
"We're thinking first of all about the health of our injured because there was a lot of blood on the ground.
"For the moment there is not much news because they have been taken to different hospitals.
"In cases like these we're thinking of those near us, of those we love because that really could have been the end of us."
French team Monaco confirmed their 22-year-old midfielder Serge Gakpe was not injured in the attack.
"Serge Gakpe, who could be reached by telephone, confirmed that he had not been hurt in this attack," read a statement on the club's official website.
Adebayor was interviewed prior to his departure for the tournament and asked whether he had any reservations about playing in the politically unstable Cabinda region of Angola.
The former Arsenal forward said: "We were born in Africa so we know what it's about. Some people might be afraid, which is normal, I can understand that.
"But I'm going back to Africa, to one of the countries on my continent, and I'm prepared for Cabinda. I will enjoy myself.
"African nations are getting better and better. We can't be like France, England or America tomorrow. Angola had a big, big war but today everybody is getting along better. They have good organisation and we hope everyone will enjoy it and come back safely."
The FA has issued a statement on the situation in Angola which read: "Following the terrible attack on the Togo national team in Angola, the Football Association is in contact with various English clubs who have players involved in the African Nations Cup.
"We will continue to ensure we are kept up to speed with all developments and do all we can to assist our clubs and those players involved.
"The FA is currently contacting various organisations, including FIFA."
Chelsea, who have Didier Drogba, Salomon Kalou, Michael Essien and John Obi Mikel away on Nations Cup duty, released a statement tonight which read: "We are sure that the national teams and federations along with the authorities are taking every necessary security precaution to ensure the safety of the players and staff."