The decision came as former prime minister Ahmed Nazif was charged in a corruption case by military prosecutors, in the first case of a former regime official facing military justice.
Judge Adel Gomaa told the Cairo criminal court that Adly and his six deputies would be tried on August 3, together with Mubarak and his two sons Alaa and Gamal, and businessman Hussein Salem who is currently abroad.
Adly, who has already been sentenced to 12 years for corruption, appeared in the dock in the first of his trials to be shown on state television.
Hundreds of protesters, including families of victims who died during the revolt, turned out for the trial of the once-feared minister, throwing stones at the convoy of vans driving him away.
Mubarak was thought to be likely tried in the Red Sea resort of Sharm el-Sheikh, where he is in custody in hospital being treated for a heart condition.
But the merger of the two trials could well see the trial back in Cairo.
Activists say they will be pushing for an announcement on the venue.
Former prime minister Nazif meanwhile was charged and ordered detained for 15 days for squandering public money and seizing state-owned land, the official MENA news agency reported.
Nazif is being investigated along with the former governor of Luxor Samir Farag and businessman Mamduh Qoleib.
The public prosecutors decided to transfer the case to their military counterparts because Farag is a retired army general, the source said.
In July, Nazif was given a one-year suspended sentence for unlawful gains in a business deal worth 92 million Egyptian pounds (15 million dollars.)
Nazif is currently in prison, pending investigation into other corruption trials.
Several former ministers, officials and businessmen associated with the old regime are currently on trial, after the ruling military vowed it would bring to justice all those found guilty of abuse.
But the process has been slammed as slow and activists have been pushing for public trials.
After the spectacular fall of Mubarak, protesters are still demonstrating for an end to the military trial of civilians, the speedy trial of officials, and the redistribution of wealth.
Protesters who took to the streets to demand Mubarak's resignation have increasingly turned their anger towards the ruling Supreme Council of the Armed Forces (SCAF) which took power when Mubarak was toppled in February.
They have accused the military council of stifling dissent and slowing down the pace of reform.
Hundreds of protesters were still camped out in Cairo's Tahrir Square and vowed to continue pushing for change.
On Saturday, fierce battles erupted between protesters and army loyalists leaving 231 injured.
The clashes came hours after Field Marshal Hussein Tantawi, the head of SCAF and Mubarak's long-time defence minister, pledged in a television address to work for a free system through fair elections and a constitution.
But the military rulers had also accused the April 6 movement, that helped launch the January 25 uprising, of "driving a wedge between the people and the army".