"Our first priority is the safety of the players but the tournament will go ahead," Confederation of African Football (CAF) spokesman Suleimanu Habubu said in Luanda.
A bus driver was killed in the gun attack on Friday shortly after the Togo team crossed the border into the Cabinda enclave, where they are due to play their first group match on Monday.
Two players were injured in the attack along with a further seven team officials, Angolan government officials said. The Togo team were seeking to return home after the attack.
"I don't know even if we will play (in) the Nations Cup," Togo midfielder Thomas Dossevi told Radio Monte Carlo.
The separatist group the Front for the Liberation of Enclave of Cabinda (FLEC) claimed responsibility for the attack, which happened two days before the start of the Jan. 10-31 tournament.
Separatists have been seeking independence for the oil-rich territory, which lies to the north of Angola but is separated from the country by the Democratic Republic of Congo.
FULL FACTS
CAF said high-ranking officials would fly to the area on Saturday. "We want to know the full facts which we don't have as yet. We cannot offer a reaction yet to the media before we have assessed the situation," Habubu told reporters.
He told Reuters Togo had failed to communicate their travel plans. The team had been preparing for the tournament in Ponte Noire in Congo, some 150km north of Cabinda.
The team crossed by bus into Cabinda after which their convoy came under fire. Midfielder Thomas Dossevi told French radio the attack had lasted some 15 minutes.
Cabinda, which has a newly-built stadium with a 30,000-seater capacity for the tournament, is also scheduled to host matches involving Ghana, the Ivory Coast and Burkina Faso.
Players due to play in the opening Group B games on Monday include Chelsea's Didier Drogba and Michael Essien.
Togo's African Footballer of the Year Emmanuel Adebayor was not injured, his club Manchester City said on Friday, but reserve goalkeeper Kodjovi Obilale and defender Serge Akakpo were wounded in the attack, Togo officials confirmed.
The stadium in Cabinda was one of four new venues built for the 16-team tournament, which starts in Luanda on Sunday.
Angola is recovering from decades of civil war and has limited infrastructure, which is being severely stretched by the number of visitors for the three-week event.
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