Businessman Hussein Salem, a close associate of the Mubarak family, is to be tried in absentia.
Mubarak was brought into court on a stretcher with a drip after being brought in an ambulance from a military airport. He had been flown to Cairo from hospital in Sharm el-Sheikh, where he had earlier refused to leave his bed.
His lawyer, Farid al-Deeb, argues that Mubarak is to ill to stand trial, claiming that he is suffering from cancer and went into a coma last month. The hospital denies that is the case, although doctors say he is extremely depressed and weak after refusing food for several days.
More than 1,000 soldiers and police provided security at the complex in a Cairo suburb. About 600 lawyers and journalists have been authorised to attend.
Supporters and opponents of Mubarak clashed briefly outside the police academy.