The move is an apparent concession to protesters who want Mr Mubarak and his allies tried for corruption.
It follows an army move on protesters in Cairo's Tahrir Square on Saturday in which at least one person was killed.
The military has said it will use force to clear the square "to ensure life goes back to normal" in Egypt.
Dozens of people were also injured in the violence in Tahrir Square early on Saturday as the army tried to enforce an overnight curfew.
They suffered gunshot wounds but the army denies using live rounds.
The violence came after hundreds of thousands of people protested in Tahrir Square on Friday, demanding the prosecution of Mr Mubarak for corruption.
More protesters returned to the square later on Saturday and remained overnight.
On Sunday morning a few hundred protesters were in the square, which was sealed off with barbed wire and closed to the usually busy traffic of the beginning of Egypt's work week.Army threat
Tensions have been growing between the military, who took control after Mr Mubarak's downfall in February, and protesters calling for speedier reforms.
Divisions have also emerged within the protest movement that forced Mr Mubarak's resignation, says the BBC's Yolande Knell in Cairo.
Some are calling for the resignation of the head of the ruling military council, Field Marshal Mohamad Hussein Tantawi, who is Egypt's interim ruler.
He was defence minister under Mr Mubarak and was very close to the former president.
Others in the protest movement fear further antagonism with the military will cause more problems for Egypt ahead of elections and a transition to civilian rule planned for later in the year, our correspondent says.
The military's move to replace a number of Mubarak-appointed provincial governors was one of the demands of protesters.
Many among the protest movement believe the military figures now overseeing political transition are protecting Mr Mubarak and his allies.
On Saturday, a general said the army was "ready" to use force to clear the square and allow normal life to resume.
"Tahrir Square will be emptied of protesters with firmness and force to ensure life goes back to normal," Major General Adel Emarah, of the military council, told a news conference.
The army had maintained a generally neutral role in the earlier mass demonstrations.
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