Authorities seized Aboutrika's shares in Tours travel company, which he co-founded in 2013, earlier this month.
The company is accused of funding the Muslim Brotherhood, which Egypt designated a "terrorist group" in December 2013.
A committee from the justice ministry charged with confiscating Brotherhood assets refused Aboutrika's appeal to reclaim his shares, judicial officials said.
Aboutrika can file another appeal to the committee, which could refer the case to prosecutors for a criminal investigation and trial, the officials added.
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In an interview with state-run Al-Ahram newspaper published on May 14, Aboutrika denied that his company or any of his partners had ever funded the Islamist movement.
The authorities have cracked down on members and supporters of the Brotherhood since July 2013, when the army ousted president Mohamed Morsi, Egypt's first freely-elected leader.
Morsi was ousted after mass protests against his sole year of divisive rule, and an ensuing police crackdown targeting his supporters and his Muslim Brotherhood movement has left hundreds dead and thousands jailed.
Aboutrika, one of the most successful African footballers of his generation, had publicly endorsed Morsi's 2012 presidential bid.
Fans of the retired footballer launched a campaign condemning the seizure of his shares.
A star of the Cairo-based club Al-Ahly as well as the Egyptian national team, 36-year-old midfielder Aboutrika retired in 2013, and has since avoided expressing his political views publicly.