The former Egyptian president was taken by ambulance to Tora prison under heavy security escort, a security source told Agence France-Presse.
Egypt's public prosecutor ordered Mubarak back to prison on Wednesday after his health was deemed stable.
Mubarak (84) was being treated for a heart condition, fractured ribs, fluid in the lungs, depression and high blood pressure, according to his lawyers and official accounts.
The transfer, however, was delayed as hundreds of his supporters gathered outside the military hospital in the Cairo suburb of Maadi in a bid to prevent his return to prison, the security source said.
Mubarak stunned many Egyptians when he appeared last Saturday at the opening hearing of his retrial, looking strong, defiant and waving at supporters.
The retrial was meant to begin on April 13, but Judge Mostafa Hassan Abdallah recused himself in an opening session that lasted just seconds and sent the case to the court of appeal to choose a new circuit.
Charges
In October, the same judge had acquitted defendants in the infamous "battle of the camels" trial who were accused of sending men on camels and horses to break up a protest during the 2011 uprising that toppled Mubarak.
Mubarak, his former interior minister Habib al-Adly and six security chiefs are charged with complicity in the murder and attempted murder of hundreds of peaceful protesters on January 25 to January 31 2011.
Mubarak's sons, Alaa and Gamal, will face corruption charges along with their father and fugitive businessperson Hussein Salem.
The new trial will open on May 11 at the North Cairo Criminal Court.
Mubarak turns 85 just days before the retrial. – AFP