His February 14 arrest came after he joined a call for a boycott of a presidential election next month that the incumbent, Abdel Fattah el-Sisi, is expected to win easily after most rivals were sidelined or withdrew.
Aboul Fotouh was detained shortly after arriving from London, where he gave interviews in which he was critical of the Egyptian government.
He was remanded in custody for 15 days and placed on the Egyptian blacklist of "terrorists".
On Sunday, the public prosecutor's office said it had decided to "sequester the assets of the Muslim Brotherhood leader (Aboul Fotouh) and other people who have been placed on terrorist lists".
It said an ongoing judicial probe had shown Aboul Fotouh's funds were being "used to carry out terrorist activities".
The interior ministry said following his arrest that Aboul Fotouh, a former leading member of the Muslim Brotherhood and candidate in the 2012 presidential election, had contacts with the group's members in exile "to sow trouble and instability".