Allaye Tessougue said: "In four of the five communes we have counted so far, Toure is in the lead with more than 50 per cent.
"The sixth commune looks likely to confirm the trend."
Toure polled between 54 per cent and 57 per cent of the vote in the four communes he had won so far, putting him well ahead of the other seven candidates.
Most of Mali's voters are outside Bamako, but winning the city is seen as the biggest challenge for Toure. His support is stronger in rural Mali, where he has focused his development efforts during his first five-year term.
The one Bamako commune that Toure, known popularly by his initials "ATT", did not win is the home neighbourhood of Ibrahim Boubacar Keita, his closest rival, national assembly president and former prime minister.
Keita has already said that electoral lists were out of date, ballot papers had been circulated before voting began and that the military had been told to vote for Toure.
But election observers and diplomats said aside from a few technical glitches, they had seen no irregularities which could undermine the credibility of the vote.