There is no second round of voting in Mexico, and the final winner in Sunday's election is to be inaugurated for a six-year term December 1 to succeed outgoing President Felipe Calderon.
Molina said the ballots from 78,012 polling centres are to be recounted, out of a total of more than 143,000.
Some 60 per cent of the ballots cast in the simultaneous legislative election are also to be recounted.
Lopez Obrador has claimed there are inconsistencies in 80 per cent of the voting centres. He alleged fraud and unfair use of the media, and accused the PRI of buying votes.
The IFE has said on Tuesday (local time) that it would recount one-third of the ballots but then increased the proportion.
Requirements for votes to be recounted in a voting centre include the presence of obvious mistakes, a difference below 1 percentage point between the top two finishers, the fact that all votes in the precinct go to a single candidate or that the number of spoilt ballots is greater than the difference between the top two candidates.
Pena Nieto's campaign coordinator, Luis Videgaray, stressed that the PRI agrees with a recount as long as it respects requirements and is not based on the "whim" of one person.
"Enrique Pena Nieto won the presidential election by a wide margin and if votes need to be recounted, let it be in accordance with the law," Videgaray said.
"Enrique Pena Nieto's triumph will be confirmed."
Lopez Obrador also challenged the results of the 2006 election, which he lost to Calderon, though the difference in that race was only 0.56 percentage points.
In their protest six years ago, Lopez Obrador and his followers cut off Mexico City's main traffic artery, Paseo de la Reforma, for several weeks. The former mayor of the capital even staged a ceremony in which he was proclaimed Mexico's "legitimate president".
On December 1, 2006, Calderon was inaugurated in a speedy ceremony amid shouts in Congress, and he could not even make his inaugural address to the legislature.
The PRI has in recent years shed its corrupt, authoritarian history. Pena Nieto has pledged to practice "a new way of governing" within democracy boundaries and "in line with the demands of the 21st century."
"We're a new generation," he said.
"There's no return to the past."
-DPA