Adly had been charged with embezzling public funds. The verdict can be appealed against before Egypt's top civil court, the Court of Cassation.
A long-serving official at the head of Egypt's feared internal security apparatus, Adly was acquitted of other graft charges two years ago. He was also cleared in 2014, along with Mubarak and six aides, of charges related to killing protesters during the 2011 uprising which had led to their downfall.
Mubarak was freed last month after six years in detention, having been cleared of the final murder charges against him.
Adly did not attend court on Saturday and his lawyer did not respond to a call for comment.
Alongside Adly, the court sentenced two other ministry officials to seven years in jail without parole, a copy of the verdict obtained by Reuters showed. It ordered the three men to refund a total of 1.95 billion Egyptian pounds ($108 million) and fined them the same amount.
A further eight officials were sentenced to between three and five years in jail.