Friday's attack, in which the driver was also killed and seven others were injured, took place in Cabinda, a province where guerrillas have fought a secession campaign for decades.
"We lost the assistant coach and the press officer," said Messan Attelou, chief spokesman for Togo's soccer federation.
He said Togo had not yet decided whether to pull out of the tournament.
"We are going now to see and talk to the players and then make a decision whether or not we take part in the competition," he told Reuters at Cabinda airport.
Togolese officials named the dead men as media officer Stanislas Ocloo and assistant coach Amalete Abalo, and said reserve goalkeeper Kodjovi Obilale had been evacuated to Johannesburg for medical treatment.
The attack came five months before neighbouring South Africa hosts the World Cup, the first African nation to hold the world's biggest single sport event.
Virgilio Santos, an official with the African Nations Cup local organising committee COCAN, said teams had been told explicitly not to travel to the tournament by road. "We asked that all delegations inform us when they would arrive and provide the passport number of their players," he told the sports weekly A Bola.
"Togo was the only team not to respond and did not inform COCAN it was coming by bus ... The rules are clear: No team should travel by bus. I don't know what led them to do this."
The Front for the Liberation of the Enclave of Cabinda (FLEC) claimed responsibility for the attack.
A shaken Togo captain Emmanuel Adebayor, who joined Manchester City for a reported 25 million pounds ($40 million) last year, said the attack would hurt the image of Africa as a whole. "We keep repeating (that) -- Africa, we have to change our image if we want to be respected -- and unfortunately that is not happening," Adebayor told the BBC World Service before leaving Angola.
"A lot of players want to leave. They have seen death and want to go back to their families," he said.
Rich Mkhondo, chief spokesman for the World Cup organising committee, said the attack had no relevance to the World Cup. "We remain confident that everyone coming to South Africa will have a safe and secure experience in our country," he said.
CAF has said the Nations Cup, which ends on Jan 31, will go ahead.