Morsi said that he had not been consulted and would pursue his own plans for national reconciliation.
He described the deadline as potentially confusing.
The army had said it will intervene if the government and its opponents fail to heed "the will of the people".
It wants President Morsi to agree on a common platform with liberal rivals whose supporters have taken to the streets demanding his resignation.
"The president of the republic was not consulted about the statement issued by the armed forces," a statement said. "The Presidency sees that some of the statements in it carry meanings that could cause confusion in the complex national environment."
It continued: "The Presidency confirms that it is going forward on its previously plotted path to promote comprehensive national reconciliation."
Millions rallied nationwide on Sunday urging the president to step down.
Those protests continued on Monday with activists ransacking Cairo's Muslim Brotherhood headquarters.
Morsi has been accused of putting the Muslim Brotherhood's interests ahead of the country's.
The Islamist assumed office on 30 June 2012.
Image: © Getty
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