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The Pharaohs secured the prestigious trophy for keeps after winning the AFCON three times in 2006, 2008 and 2010.
However, the trophy which was kept at the FA’s headquarters in Cairo is said to have mysteriously gone missing.
Former EFA Vice President Ahmed Shobeir confirmed the disappearance of the trophy while speaking on the 'On Time Sports' TV show.
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Egypt secured the AFCON for keeps after winning it from 2006 to 2010
"The EFA started looking for some trophies as they aim to put them in a notable museum inside the EFA," he said.
"However, the EFA was surprised to find that the AFCON trophy was lost and decided to open an investigation.
"They were informed by an employee inside the association that it was held by former Egypt captain Ahmed Hassan who refuted this claim. Nobody knows where the trophy is at the time being."
Meanwhile, ex-Egypt midfielder Ahmed Hassan who captained the Pharaohs to the three successive AFCON titles,refuted claims that the trophy was with him.
"I wish I had kept the cup in my house instead of it being lost and I am surprised that I'm being questioned about the cup after nine years, despite the presence of two FA boards, and the five-year committee for a year and two months...but they're only now looking for the cup!” he wrote on Twitter.
Egypt is the most successful side in the history of the AFCON, having emerged champions a record seven times.