A team from General Prosecutor Hisham Barakat's office was ordered to prepare a study with reasons to be proposed to the appeal court.
"A study of the reasons for the ruling revealed legal flaws that marred the judgment," said a statement issued by the general prosecutor's office.
On Saturday, the Court of Cassation, Egypt's highest court, ruled that 86-year-old Mubarak and seven of his former security commanders, including his former interior minister Habib al-Adly, were "innocent" in the killing of anti-government protesters during the 2011 Egyptian Revolution. The judge in the case said that Mubarak should never be tried for these charges.
Last week's judgement overturned the life sentence Mubarak received in June 2012, and means he will face no punishment for allegedly sanctioning the murder of 846 protesters during Egypt's 2011 uprising that ousted him or for allegedly profiting from the export of gas at below-market rates.
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Mubarak's sons, Alaa and Gamal, currently serving four-year prison terms for embezzlement of state funds, were also acquitted on all corruption charges.
The ruling was followed by massive angry protests in Cairo in which two people were killed.
In 2012, the former dictator was sentenced to 25 years in jail but the verdict was successfully appealed in January, 2013 as the presiding judge ruled that there was not enough evidence presented by the prosecution. Mubarak's retrial began in April, 2013.
Though Mubarak was not convicted on any charges, he will still not be freed as in May, a Cairo court had sentenced him to three years in prison for embezzlement.
Mubarak is serving his sentence at a military hospital on the southern outskirts of Cairo.