The Togo team bus came under gunfire attack from separatists fighting for the independence of Cabinda at a border crossing near the frontier with Congo.
The Togolese players have insisted that they would like to stay and participate in the African Cup of Nations in order to honour the three people who were killed in the attack.
The separatist guerillas responsible have threatened more attacks. The opening game of the tournament between Angola and Mali kicks off tonight.
"We understand the approach of players who wanted to express a way to avenge their fallen comrades, but it would be irresponsible on the part of the authorities to let them continue," Houngbo said, according to L'Equipe.
"The team must return today. The government's decision is unchanged.
"It is a conscious decision since Friday. If a team or a person present themselves under the banner of Togo, it would be a false representation."
"It is left to you to decide to stay in a competition synonymous of fraternity, brotherhood, friendship and solidarity.
"And in case you decide to leave the competition, we will definitely understand your decision and it will be accepted."
England manager Fabio Capello's assistant Franco Baldini will still
travel to the tournament on a scouting mission this week, despite
Friday's tragic events and the threat of more attacks.
Capello's recent knee operation means that he cannot make the trip in person, but Baldini could still travel in his place.
He is under no obligation to go, and the British government have advised citizens only to travel to Angola if absolutely necessary.
Zack Wilson, Goal.com UK