Edmundo Jacopo Molina, executive secretary of the Federal Election Institute, said the parties can monitor the recount, CNN reported. He said 78,012 boxes, or 54.5 percent of the total, will get hand recounts.
While unofficial results give Enrique Pena Nieto, candidate of the Institutional Party of the Revolution, or PRI, a margin of victory between 6 percentage points and 7.65 percentage points in Sunday's voting, the runner-up, Andres Manuel Lopez Obrador, has not conceded.
His supporters in the Party of the Democratic Revolution, or PRD, accuse the PRI, which governed Mexico as a one-party state for decades until 2000, of engaging in old-style election fraud.
Daniel Avila of the student-led Twitter movement #YoSoy132 said the group has received more than 1,000 reports of fraud, including the stuffing of ballot boxes and intimidation of voters.
The PRI also used gift cards from a retail chain to win support, Lopez Obrador's supporters say.
The candidate of the National Action Party or PAN, which has governed Mexico for the past 12 years, came in third.