"If a team or some people present themselves under the Togolese flag, it will be a false representation," Gilbert Houngbo told journalists in the capital Lome.
A player and a Togo soccer official in Angola had insisted earlier that the team would play in the African Nations Cup due to open later on Sunday.
"Togo are staying in the competition. I have called the players and they want to play. We are now awaiting official confirmation from the Togolese government," said Kodzo Samlan, general secretary of the Togo soccer federation and a press officer for the Confederation of African Football (CAF).
He added that Togo team captain, Emmanuel Adebayor, was with the team in Angola’s Cabinda enclave. English Premier League club Manchester City had said on its website on Saturday that Adebayor, its star striker, was returning to Britain.
The team’s media officer Stanislas Ocloo and assistant coach Amalete Abalo were killed along with the bus driver. Seven people were wounded including reserve goalkeeper Kodjovi Obilale, who is in a stable condition in a South African hospital after surgery.
Early indications on Sunday were the players had determined to be ready for their first Group B match on Monday, and witnesses saw the team practicing on Sunday morning.
"We have just had a meeting of the whole delegation and we will be on the pitch on Monday to face Ghana," French sports newspaper L’Equipe on Sunday quoted midfielder Alaixys Romao.
"People have died for the African Nations Cup, others have been injured. We can’t let them down and leave like cowards," said Romao, who plays for French club side Grenoble.
"Our government does not necessarily agree with us but we are all determined to play this competition."
Angola has spent $1 billion building stadiums, roads and hotels for the competition, which brings together Africa’s best national teams. The bi-annual tournament, which lasts until January 31, will be broadcast live around the world.
The African Nations Cup is due to start with fireworks and champagne at a massive stadium in the capital Luanda, where the hosts play Mali in the opening match later on Sunday.
But Friday’s attack on the Togo team, staged by the Front for the Liberation of the Enclave of Cabinda which the government said recently no longer existed, cast a shadow over an event supposed to show Angola was at peace after years of civil war.
Security analysts said the ambush showed how easily insurgents can grab world headlines.
Cabinda, the scene of FLEC attacks even after Angola’s 27-year civil war ended in 2002, provides half the oil output of Angola, which rivals Nigeria as Africa’s biggest producer.
It was the second militant attack on a sports team in less than a year. Last March, six policemen and a driver were killed when gunmen attacked a bus carrying Sri Lanka’s cricket team in Pakistan.
Friday’s assault raised questions about security for the soccer World Cup taking place in South Africa in June, but organisers of that event dismissed any comparisons. South Africa is the first African nation to hold the world’s biggest single-sport event.
Security analysts said outsiders involved in the World Cup are unlikely to ignore the Angolan attack and will want to review South Africa’s security preparations.
South African President Jacob Zuma will attend Sunday’s opening ceremony despite the attack, his spokesman said.
Cabinda, wedged between the Democratic Republic of Congo and Republic of Congo, was due to host seven matches.