Adel al-Khayat, a member of Al-Gamaa Al-Islamiya, blamed his resignation on "an unjust media campaign" against him, Al Ahram newspaper reported.
Khayat's appointment triggered controversy due to Al-Gamaa Al-Islamiya's role in the murder of at least 58 tourists and 4 Egyptians in a terrorist attack in Luxor in 1997.
President Mohammed Mursi infuriated many by appointing Khayat last Monday, reaching out for a political alliance with the more radical party ahead of a big wave of opposition-led protests on June 30, the paper said.
His appointment also served a blow to tourism which is already suffering because of the security lax.
Luxor is one of the main tourist attractions and contains the most important Pharaonic monuments.
As the site of the Ancient Egyptian city of Thebes, the city has frequently been described as the "world's greatest open air museum", as the ruins of the temple complexes at Karnak and Luxor stand within the modern city.
