Authorities in Angola had moved quickly to ensure they were doing everything possible to safeguard the tournament, which opens on Sunday.
"We are going to further reinforce all the mechanisms and continue to guarantee security and create all the conditions which guarantee the success, and organisation and safety of poeple as planned," Goncalves Muandumba, Angola's minister for youth and sport, said.
After seeing the aftermath of the attack, members of the Mozambique national team flying into Luanda were seeking assurances of protection.
"Of course I think that it is very worrying," Otshudi Lam, a player, said.
"Today we are boarding for Angola, am I afraid? Yes, I'm afraid."
Amade Chababe, the assistant coach of the Mozambique team, said: "We have goosebumps.
"Because with these attacks we cannot say that it only happens to Togo. Who knows what is going to happen to us?"
Organisers have said that the tournament, which is due to kick off on Sunday, will go ahead, but African football officials met the Angolan government beforehand to seek assurances that players would be protected.
Al Jazeera's Andy Richardson, reporting from Luanda, said that he expected that players from most nations would be considering their participation despite the organisers' assurances.
"I think a lot of players involved here, a lot of clubs that they play for, and obviously their families back home, are not as convinced as officials," he said.
"There are some multimillion-dollar players up there in Cabinda and a lot of them have clubs back in Europe who are obviously very concerned about them being exposed into an area where it seems security cannot be guaranteed."
Cote d'Ivoire, Burkina Faso and Ghana were also to be based in Cabinda, which is separated from the rest of Angola by a slice of Democratic Republic of Congo, for the tournament.
The Togo team had been training in DR Congo and were travelling to Angola by bus ahead of their match against Ghana on Monday.
However, local official questioned why the team were travelling by bus rather than air.
"The rules are clear: no team should travel by bus. I don't know what led them to do this. The incident would not have happened in the city," Virgilio Santos, an organising official, was quoted by A Bola newspaper as saying.
The Front for the Liberation of the Enclave of Cabinda (Flec), which has been fighting for independence for three decades, claimed responsibility for the attack, saying it was aimed at the team's military escorts.
"This operation is only the start of a series of targeted actions that will continue in all the territory of Cabinda," it said in a statement on Portugal's Lusa news agency.
Flec signed a peace deal with Angola's government in 2006, but in recent months has claimed a spate of attacks on the military and foreign oil and construction workers in the province.
Kier Radnedge, from World Soccer magazine, told Al Jazeera the decision by the Togo team was not entirely unexpected.
"You can understand the players' position entirely," he said.
"They had a terrible experience and the natural reaction is to get out of there as soon as possible".
When asked about the wider context of how the attacks on the team might impact the World Cup which takes place in South Africa later this year he replied:
"South Africa have worked very hard over the past four or five years to try to dispel the idea that there was a security problem about the world cup in south Africa…now security has gone right back to the top of the visibility agenda."