The party's Secretary-General Safwat El-Shari, Minister for Parliamentary Affairs Mufid Shehab and Chief of the presidential staff Zakaria Azmi also resigned.
The party's new Secretary-General Hossam Badrawi is seen as a member of the party's liberal wing.
It seems this latest step joins earlier measures, including rapprochement between Vice President Omar Suleiman and opposition leaders.
President Mubarak recently told ABC he wanted to resign but fears his resignation will cause chaos.
Suleiman promised Gamal Mubarak will not participate in the upcoming presidential elections.
In an attempt to appease protestors, many bank accounts of officials, including those of the former interior and tourism ministers, have been frozen.
Earlier on Saturday, an Egyptian army commander addressed thousands of Egyptians camped out at Tahrir Square in central Cairo in an effort to persuade them to stop a protest that has stalled economic life in the capital.
"You all have the right to express yourselves but please save what is left of Egypt. Look around you," Hassan al-Roweny said using a loud speaker and standing on a podium.
Demonstrators continue to gather at Tahrir Square, though the last couple of days have been relatively quite.
Reuters contributed to this report
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