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"The government is maintaining its decision to call the team back home," administration minister and government spokesperson Pascal Bodjona told AFP.
Hours before the competition starts on Sunday, players said they wanted to stay in Angola.
"In memory of the dead, the national team has decided to play in the Africa Cup of Nations," Thomas Dossevi, who plays for French side Nantes, told AFP.
But Bodjona said "the best thing to do is not to stay".
"People are dead. The goalkeeper (Kodjovi) Obilale is in intensive care," he said.
Hooded gunmen opened fire on the teams' buses as they crossed into the restive Angolan enclave of Cabinda, killing the assistant coach and squad spokesperson.
The attack was claimed by a faction of the Front for the Liberation of the Enclave of Cabinda (FLEC) separatist group embroiled in a struggle for independence in the oil-rich territory.
In earlier reports it was stated that the prime minister of Togo, Gilbert Houngbo, on Sunday ordered the national football team to immediately return home from the Africa Cup of Nations after a deadly attack.
"If there is a team or persons present under the banner of Togo at the opening of the African Nations Cup this afternoon, it will be a false representation. The team must return today," he told reporters.
"We understand the position of the players who want to in some way avenge their dead colleagues, but it would be irresponsible for the Togolese authorities to allow them to continue," he added.
"The team must come home. The government's decision is unchanged."
