Officials say the shooting occurred in the Angolan oil-rich territory of Cabinda, where rebels have been fighting for independence.
The Angolan government called the incident an "act of terrorism". There are reports of serious injuries.
Togo is due to play its first cup game in Cabinda on Monday.
Manchester City striker Emmanuel Adebayor was on the bus but is unhurt. In a statement, Manchester City said Adebayor had been "shaken by the terrible events" but was "unharmed".
Adebayor was on the bus but escaped injury
The bus was travelling to Cabinda from the squad’s training ground in the Republic of Congo when the shooting happened.
"This was an act of terrorism," Cabinda affairs minister Bento Bembe told Reuters news agency.
Competition officials said they had not known that the Togolose team had decided to drive directly to Cabinda.
They said they had expected the squad first to fly to the Angolan capital, Luanda, and from there to Cabinda.
Shot ‘like dogs’
Togo striker Thomas Dossevi told France’s RMC radio that several players were "in a bad state" after the attack.
Oil-rich province cut off from the rest of Angola by DR Congo
Flec rebels fought for region’s independence
Rebels laid down arms in 2006 but some unrest continues
Angola had dismissed concerns about staging games there
"We were machine-gunned, like dogs," he said. "At the border with Angola – machine-gunned! I don’t know why. I thought it was some rebels. We were under the seats of the bus for 20 minutes, trying to get away from the bullets."
The identities of those injured – who also included team staff – are not known.
Togo are due to play Ghana, Burkina Faso and Ivory Coast in their group matches. Their first game is against Ghana.
Midfielder Alaixys Romao told RMC Togo were now likely to pull out of the 16-nation tournament.
"No-one wants to play," he said. "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."