Egyptian special services arrested al-Filali in 2000 on charges of supplying Israel's Mossad with military, political, and economic information about Egypt in exchange for money. Israel denied any involvement.
Sherif al-Filali was first acquitted of the charges in 2001 but convicted a year later in a retrial ordered by President Hosni Mubarak.
The cause of al-Filali's death is being investigated.
Al-Filali was one of several Egyptians recently convicted over providing Israel with sensitive information. In late June, an Egyptian engineer at the state Atomic Energy Agency received a life sentence for passing documents about a nuclear reactor.
Earlier this year, another man with dual Egyptian-Canadian citizenship was sentenced to 15 years in prison and fined about $1,500 for spying for the Jewish state. Investigators said the man had gathered information on Arabs living in Turkey and Canada for the Israeli secret service.