Felipe Calderon was informed by the Federal Electoral Institute that according to electoral law, the ballots must be destroyed once a winner is declared.
The center-right Calderon won a closely contested race against left-wing former Mexico City Mayor Andres Manuel Lopez Obrador, who lost July's election by less than 1 percent of the total vote and has contested the results.
Obrador has led numerous protests in the capital and promised to create a parallel government.
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