The previously concealed architectural elements reveal well-preserved hieroglyphics and unique scenes depicting the powerful pharaoh.
The discovery is likely to touch a nerve among religious leaders, because the newly exposed reliefs contain representations of humans and animals, which are forbidden inside mosques, the experts said.
The mosque was erected as a shrine to Muslim saint Abul Haggag in the 13th century A.D. on the site of an earlier Christian church, which was itself built on top of the ancient temple, the archaeologists explained.
The discovery was made during repair work on the mosque after a fire damaged part of the structure in June.
"To do this project of restoration, [workers] had to reclean and reopen many things, and this is when the scenes were found, and they are really unique," said Zahi Hawass, secretary general of Egypt's Supreme Council of Antiquities.
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