In a statement issued on Monday, the office said that some phrases in the ultimatum could create confusion, AFP reported.
It said it denounces “any declaration that would deepen division” and “threaten the social peace” in the country.
The statement added that the presidency would continue on its own path towards national reconciliation.
President Morsi was consulting “with all national forces to secure the path of democratic change and the protection of the popular will,” according to the statement.
“The civil democratic Egyptian state is one of the most important achievements of the January 25 revolution,” it pointed out, nothing that “Egypt will absolutely not permit any step backward whatever the circumstances,” it said.
Earlier in the day, Egypt’s army said it would intervene if Morsi and his opponents fail to resolve the crisis in the country in 48 hours.
On Sunday, millions of Egyptians demonstrated in cities nationwide to demand Morsi’s resignation and early presidential elections.
The country’s Health Ministry said 16 people were killed in Sunday’s demonstrations.
The massive protests on Sunday came on the first anniversary of Morsi’s inauguration as president following the 2011 revolution that toppled the Western-backed regime of former Egyptian President Hosni Mubarak.
The protests continued on Monday. The opposition movement behind the protests — Tamarod (Arabic for Rebellion) — has given Morsi until 5:00 p.m. (1500 GMT) on Tuesday to step down and call fresh presidential elections, or else face a campaign of civil disobedience.
Several political groups say the government is dominated by the Muslim Brotherhood. The opposition also accuses Morsi of deviating from the 2011 revolution.