Mexican electoral authorities are recounting more than half the ballot boxes used in the weekend's presidential election after finding inconsistencies in the vote tallies.

Of the 143,000 ballot boxes used during Sunday's vote, 78,012 will be opened and the votes recounted, Edmundo Jacobo, executive secretary of Mexico's Federal Electoral Institute, said Wednesday.

Jacobo said the recount could be finished by Thursday.

Mexico's electoral law states that votes should be recounted if there are inconsistencies in the final tally reports, if there is a difference of one percentage point or less between the first and second place finishers or if all the votes in a ballot box are in favour of the same candidate.

Electoral workers recount votes at a district office of Mexico's Federal Electoral Institute in Acapulco Wednesday. (Jacobo Garcia/Reuters)

With 99 per cent of the vote tallied in the preliminary count, Enrique Pena Nieto of the Institutional Revolutionary Party, or PRI, led with 38 per cent of the vote. Andres Manuel Lopez Obrador of the Democratic Revolution Party had 32 per cent.

Authorities also will recount 61 per cent of the ballot boxes in the vote for senate seats and 60 per cent in the vote for the lower house of congress, Jacobo said.

The presidential front-runner expressed confidence Wednesday about the recount. "I trust that the final tally will be consistent with the preliminary count," Pena Nieto said.

Lopez Obrador has refused to accept the preliminary vote tallies, saying the election campaign was marred by overspending, vote-buying and favourable treatment of Pena Nieto by Mexico's semi-monopolized television industry.

The leftist candidate said Tuesday that his team had detected irregularities at 113,855 polling places, and called for a total recount.

Vote-buying allegations

Feeding suspicion of large-scale vote-buying were scenes of thousands of people rushing to grocery stores this week to redeem pre-paid gift cards they said the PRI had given them ahead of the election. Several told reporters they had been told to turn in a photocopy of their voter ID card in order to get the gift cards.

Under Mexican election law, giving voters gifts is not a crime unless the gift is conditioned on a certain vote or is meant to influence a vote. However, the cost of such gifts must be reported, and cannot exceed campaign spending limits. Violations are usually punished with fines, but generally aren't considered grounds for annulling an election.

Shoppers nearly stripped some shelves at a Soriana store in the poor district of Iztapalapa and officials in Mexico City, which is governed by Democratic Revolution, ordered at least one branch of the chain closed for alleged violation of safety codes.

Both the PRI and the supermarket company denied any irregularities.

PRI spokesman Eduardo Sanchez said that "Neither the PRI's executive committee, nor Enrique Pena Nieto's campaign has contracted any service from the Soriana grocery store chain."

Asked if some other local or congressional PRI candidate could have done it on behalf of Pena Nieto, he said "I don't know."

Humberto Fayad, a spokesman for the Soriana chain, denied the company had sold huge amounts of gift cards to the PRI.

"There is no agreement between the PRI and Soriana, or Soriana and any other political party. Soriana is a non-political company," Fayad said.

The PRI, too, accused rivals in many parts of the country of handing out groceries or using government programs to influence voters.

The governing National Action Party accused Pena Nieto's campaign of acquiring about 9,500 prepaid gift cards worth nearly $5.2 million US (71 million pesos) to give away for votes. Authorities said a business had bought that number of cards, but that they had found no direct evidence of vote-buying. That investigation continues.

On Tuesday, Alfredo Figueroa, a council member of the Electoral Institute, said authorities were investigating complaints about the Soriana gift cards. Members of the institute have said they were aware of attempts to engage in vote buying.