Faure Gnassingbe, who was named president by the army last Saturday hours after the sudden death of his father, was not part of the delegation, which was summoned to Niger by West African leaders who have condemned the takeover as a coup.
Interior Minister Francois Boko said soldiers sent to break up an opposition protest in Lome had fired warning shots to disperse a crowd which had surrounded their vehicle in the neighbourhood of Be, an opposition stronghold.
Two demonstrators were killed on the spot, he said, and a third died later in hospital.
A government statement read out on state television said two paramilitary gendarmes had been seriously injured. It appealed for calm, and said one soldier involved in the killing of the protesters had been detained.
One of the protest's organisers said security forces had shot dead four demonstrators. "The number of dead people who have been identified is four. There have been several injured, but we don't know how many," said Martin Aduayom.
By late afternoon, calm appeared to have returned to the streets of Lome. Soldiers, police and members of an elite unit known as the Red Berets manned the city's main intersections.
Gnassingbe was not part of the
delegation to Niger
Witnesses said earlier about 2000 people had gathered in Be with banners reading "Togo is not a monarchy" and "The coup d'etat will not succeed".
Police initially fired tear gas and stun grenades to disperse them, saying they were only obeying orders from the Interior Ministry, but the opposition said security forces had also used live ammunition.
Some protesters hurled stones at the police and then set up makeshift barricades using old cars and burning tyres.
The government has banned all public demonstrations for the two-month mourning period after the death of Gnassingbe Eyadema, Africa's longest-serving leader.
Gnassingbe's appointment violated the constitution, which parliament hastily amended afterwards to legalise the move and clear the way for him to rule until 2008.
At least three people were killed
in clashes in the capital
African leaders, former colonial ruler France and the United States want the takeover to be reversed and presidential polls held. The African Union (AU) and the Economic Community of West African States (ECOWAS) have threatened sanctions.
A Togolese delegation headed by Prime Minister Koffi Sama and including representatives of the army, parliament and the constitutional court, were in a closed-door meeting with Niger's President Tandja Mamadou, who currently chairs ECOWAS.
But an aide to Mamadou, who asked not to be named, said there would be no negotiations with the Togolese.
"There won't be negotiations. The president will just tell them what ECOWAS's position is," he said ahead of the talks.
The heads of state of Nigeria, Niger, Mali, Ghana and Benin had been due to travel to Togo on Friday, but cancelled the trip after a row over the venue of the talks and ordered the Togolese to go to Niger, threatening sanctions in case of a no-show.
Togo's transfer of power has dealt a blow to the declared efforts of African heads of state to prove that the continent is able to govern itself and impose democratic principles.
Under the original constitution, the head of the national assembly, Fambare Ouattara Natchaba, was supposed to take over in the event of the president's death, pending polls.