Voters want change after 38 years of rule by the same man
The attackers, some in military uniform, took computers which the opposition was planning to use to collate results from the day's polling.
Supporters of opposition candidate Bob Akitani say the ruling party is trying to rig the vote in favour of the late president's son, Faure Gnassingbe.
Mr Gnassingbe dismissed the claim but said he was convinced he would win.
The Togolese military briefly installed Mr Gnassingbe, 39, as head of state immediately after his father's death in February, but backed down amid an international outcry.
Blow to transparency
Witnesses said the raiders arrived in two pick-up trucks, threatened the people in the office with pistols and carried away the computers.
Under the Togolese electoral system, party representatives present at the count are given copies of the results, which can then be collated to give each party an independent way of verifying the declared results.
Until problems started surfacing during the afternoon, voting had mostly been going smoothly, with none of the violence that marred the election campaign.
Long queues formed during the day at polling stations in Lome and a high turnout was reported as people flocked to choose a successor to the late President Gnassingbe Eyadema.
At least seven people were killed in violence in the run-up to the election.
Less than three days before the vote, Togo's interior minister was sacked after warning of a possible bloodbath and urging the acting president to call off the ballot.
After the warning, one of the four candidates, Nicolas Lawson, withdrew from the race.
Hope for change
The front-runners are Mr Gnassingbe and Mr Akitani, a 74-year-old veteran opposition activist.
Harry Olympio, a minister under Gen Eyadema, also stood.
Casting his vote in Lome, Mr Gnassingbe expressed confidence in the outcome, but added: "I don't want to stay in power forever, I won't do 38 years" - a reference to his father's long tenure.
Whoever wins, Togo will not be the same, analysts say
The US has said the international community will be scrutinising Togo's balloting and vote-counting process.
International pressure forced Mr Gnassingbe to back down from his taking of power and play by the constitutional rules by calling the election.
Party representatives descended on polling stations to monitor the vote, as did veteran politicians from the regional grouping, Ecowas.
Mr Akitani alleged widespread voting fraud, in remarks to the AFP news agency.
"The stuffing of ballot boxes is occurring on a large scale and we haven't heard of a single polling station where everything is going well," he said.
For most of the time since independence, Togo has been under either military dictatorship or one-party rule and both the most recent elections have been marred by allegations that the ruling party cheated to keep itself in power.
Segundo reporte da rádio australiana SBS se reportaram três mortos em incidentes de violência relacionados com os protestos por fraude nas eleições em Togo, nação do oeste da África. As eleições se levaram a cabo para eleger um presidente em substituição de Gnassingbé Eyadéma, quem governa há 38 anos.

Há três candidatos para a eleição: o filho do presidete, Faure Gnassingbé, Emmanuel Akitani Bob de 74 anos, e Harry Olympio, primo do governante de Togo derrocado e assassinado pelo falecido presidente (segundo sua própria declaração) em 1963. Um quarto candidato, Nicolas Lawson, estava também inscrito mas se retirou dois dias antes da eleição por "temor à fraude preparada", segundo sua declaração à agência de notícias Voz da América.

O anterior governante morreu em fevereiro deste ano enquanto era transportado de emergência para receber cuidados médicos. O exército togolês apoiou uma não muito clara sucessão de poder para Faure Gnassingbé, que recebeu um verniz de legalidade obrigado a exercícios de leis realizados pela assembléia para destituir ao presidente da assembléia, Fambare Natchaba Ouattara, e nomear em seu lugar ao filho do falecido presidente. Faure Gnassingbé tinha informado que completaria o período de seu pai, mas a pressão internacional o obrigou a convocar a eleições.