Former army officer turned jihadist Emad al-Din Abdel Hamid had commanded the group that killed at least 16 policemen in an October 20 Western Desert ambush and later died in military air strikes, the ministry said in a statement.
The group had been organised in the Libyan militant stronghold of Derna, the ministry added.
A previously unknown jihadist group calling itself Ansar al-Islam -- or "Supporters of Islam"-- had said one of its leaders, Abdel Hamid, was later killed in the air strikes.
"The group...was formed under the leadership of Emad al- Din Ahmed Mahmoud Abdel Hamid, who died in the air strikes targeting the group" that carried out the October 20 ambush, the statement said.
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It added that the group was involved in a massacre of Coptic Christians south of Cairo in May, although the Islamic State group had claimed responsibility for that attack.
Egyptian police had for years been seeking Abdel Hamid.
Ashmawy, who split with an Egyptian jihadist group that claimed allegiance to the Islamic State group in 2014, is thought to be aligned with Al-Qaida.
Egypt believes the militants have been plotting attacks from the jihadist stronghold of Derna.
Since Egypt's army removed Morsi from power in 2013, extremist groups have increased their attacks on the military and police.
Authorities are fighting against the Egyptian branch of the Islamic State group in the north of the Sinai peninsula, over 500 kilometres away from the scene of the October ambush.
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