President Gnassingbe was installed by the military before the 2005 vote
European Union observers at Togo's presidential election have raised concerns about a lack of transparency in the collation of results.
European Parliament mission leader Michael Gahler said it had not been possible to track results after they were read out at polling stations.
The opposition has already voiced its concerns about irregularities.
The Union of Forces for Change (UFC) says it was cheated of victory by President Faure Gnassingbe in 2005.
The UFC's Jean-Pierre Fabre is trying to prevent President Gnassingbe from winning a second term.
BBC West Africa correspondent Caspar Leighton says the counting of votes in polling stations is generally believed to have been correct but Mr Gahler says the detail is starting to go at the next level - when results were transmitted to local offices of the national electoral commission.
"We had recommended that they would, on the local election office level, publish the individual results and not only the accumulated results.
"That unfortunately was not done and so we urge for transparency on all levels."
Togo's electoral commission now says a provisional result should be published by Saturday evening.
Many local observers do not feel that the independent electoral commission is truly independent and is subject to pressure from the ruling party.
But the commission's vice-president, Jean Claude Homawoo, who is from the UFC, says the commission does operate freely.
"If the result is in the favour of the opposition or of the government party, we'll take it as it comes."
The Rally of the Togolese People (RPT) party has been in power for 40 years.
Our correspondent says its heritage under the current president's father Gnassingbe Eyadema is profoundly undemocratic.
Mr Gahler thinks that President Gnassinge is, however, interested in the true verdict of the people
But he said structures around him, including the military, may think otherwise.
Our correspondent says that President Gnassingbe is both the product and the lynchpin of a system that is used to the exercise of power.
He says the opposition feels it has been cheated of victory too many times and should win this time.
It says ballot papers did not have serial numbers, only the stubs did, and these could be used to stuff ballot boxes from elsewhere.