Interim President Abbas Bonfoh sacked Interior Minister Francois Boko, who had issued a surprise call for the ballot to be cancelled because of fears of bloodshed.
The polls will go ahead as planned on Sunday, Bonfoh told Radio France International on Friday.
Warning of violence and saying the poll would be "suicide", Boko, who is in charge of security, called a news conference in the capital, Lome, on Friday to make a public appeal to cancel the vote.
Many others had called for the vote to be put off, including church groups, lawyers and the main opposition candidate, Bob Akitani.
Despite the call for a postponement on Friday, Akitani has not pulled out of the race.
The apparent split within the government comes amid mounting tensions in the tiny West African nation.
There was no immediate response from the generals who wield much of the power here or the late dictator's son, who is expected to win the race.
Faure Gnassingbe is the ruling
Violent demonstrations have continued, with many in the Togo's opposition movement vowing to die fighting if ruling party candidate Faure
Gnassingbe wins the vote.
Rioting over the weekend between the ruling party and opposition supporters left seven people dead amid escalating tensions after the 5 February death of dictator Gnassingbe Eyadema, who ruled Togo for 38 years.
Faure Gnassingbe, Eyadema's son, is up against Akitani and two other contenders, Nicolas Lawson and Harry Olympio.
After Eyadema's death, Togo's military installed Faure Gnassingbe in power in what many considered a coup.
But after intense domestic and international pressure, Faure stepped down and promised elections in 60 days, as called for by the constitution.
Bonfoh, the deputy parliamentary speaker, was appointed interim president.
In the lead-up to the vote, the opposition parties had said that registration was full of irregularities and that they hadn't been involved in the electoral process.