If convicted, Mubarak could face a life sentence or have it reduced. Under Egyptian law, a defendant cannot face a harsher sentence in a retrial, meaning the former leader cannot face the death penalty.
A new trial for Mubarak could further unsettle the nation at a perilous time.
Egypt is grappling with an ailing economy — the pound's value is slipping against the U.S. dollar, foreign reserves are shrinking and tourism is in a deep slump. And politically, the country is deeply divided by the bitter rivalry between its Islamist rulers and their allies and an opposition led by liberals and secularists.
Clashes between the two sides have left at least 10 people killed and hundreds wounded last month.
The judge also ordered a retrial of Mubarak's former security chief, Habib el-Adly, convicted and sentenced to life in prison on the same charges.
He also ordered the retrial of six of el-Adly's top aides who were acquitted in the same trial. Five of them were found not guilty of involvement in the killing of the protesters, while one was acquitted of "gross negligence." No date was set for their retrial either.
It also granted the prosecution's request to overturn not-guilty verdicts on Mubarak, his two sons and an associate of the former president, Hussein Salem, on corruption charges. Salem was tried in absentia and remains at large to this day.
The six top police commanders held key positions at the Interior Ministry, which was led by el-Adly and which is in charge of the security forces. Their acquittal surprised many Egyptians who are still demanding retribution for the nearly 900 protesters killed during the 18-day uprising that culminated with Mubarak's ouster on Feb 11, 2011.
The prosecutors in the Mubarak trial complained that security agencies and the nation's top intelligence organization had not cooperated with their investigation, leaving them with little incriminating evidence against the defendants. During the trial, prosecutors focused their argument on the political responsibility of Mubarak and el-Adly.
Sunday's ruling came one day after a prosecutor placed a new detention order on Mubarak over gifts worth millions of Egyptian pounds he and other regime officials allegedly received from Egypt's top newspaper, Al-Ahram, as a show of loyalty while he was in power.
The public funds prosecutor ordered Mubarak held for 15 days pending the completion of the investigation. Mubarak was moved to a Cairo military hospital last month after slipping inside a prison bathroom and injuring himself.
Mubarak's sons, one-time heir apparent Gamal and businessman Alaa, are in prison while on being tried for alleged insider trading and using their influence to buy state land at a fraction of its market price.