The 85-year-old, who was deposed in February 2011, had suffered high blood pressure, Egyptian daily Al-Masry Al-Youm reported.
Mubarak, his former interior minister Habib Al-Adly and six top security aides were acquitted of the charges in January last year on procedural grounds after being convicted in June 2012 following his first trial.
The retrial was scheduled to include testimony by the former head of the military police, Hamdy Badeen.
Mubarak was treated in 2010 for cancer of the gallbladder and pancreas.
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Following their conviction in the first trial, Mubarak and Al-Adly were sentenced to life in prison.
Mubarak has been in a military hospital in Cairo since he was freed from prison in August after the maximum pre-trial detention period expired.
Alaa and Gamal are already on trial with their father in the murder and corruption case, along with seven of Mubarak's former security commanders.
Egypt has been gripped by political turmoil since the overthrow of Mubarak and later under its first democratically elected President Mohammed Morsi of the Muslim Brotherhood.
Morsi's term was plagued by political uncertainty and violence in a deeply polarised country that ultimately led to his ouster by the powerful military on July 3 following mass protests against his rule.