The Egyptian Football Association,on Friday confirmed the trophy's loss the media - said it had opened an investigation into the loss of the various trophies.
"As the Egyptian FA is currently developing the main headquarters, including changing the entrance to a small museum of Egyptian football, the management was shocked by the disappearance of some old trophies from the storeroom," said the EFA in a statement.
"The EFA is now investigating the trophies' disappearance to determine if those old trophies were saved after the building was burned ... or if they were lost when the building was exposed during this incident," the EFA added.
After the EFA headquarters were attacked in 2013, various trophies - including the Nations Cup - were moved to a storeroom.
However, local officials only searched for them recently after the decision to renovate the EFA's entrance so that Egypt's multiple football cups could be displayed there.
Egyptian Pharoahs won the AFCON title in three consecutive editions in 2006, 2008 and 2010, hence awarded the trophy for keeps.
However, achievement under the guidance of legendary coach Hassan Shehata was purportedly stolen a decade ago.
Reacting to the development, CAF has stated they will render support to the EFA to recover the missing trophy.
“CAF has learnt with shock reports of missing AFCON trophies from the Egyptian Football Association secretariat.
“Our doors are open and the @EFA can count on our support in the search for the priceless memorabilia.”