Over two days, the Egyptian Armed Forces have killed 16 militants and arrested four others, said al-Rifai in a statement on Sunday.
The raid comes while the country is launching a massive counterterrorism anti-terror campaign named "Comprehensive Operation Sinai 2018" that started on Friday.
Sixty-six targets, arms depots, SUVs and motorbikes used by militants were destroyed in raids focused mainly in Sinai, but also in the Nile Delta and the western desert, the army added in a statement carried on state TV.
Authorizing troops to use "all brute force" necessary to restore "security and stability" to the region within three months, suspicion for that attack fell on an affiliate of the Islamic State (IS) group in Sinai.
The military said its warplanes struck "terrorist concentrations and hideouts" in northern and central Sinai through the night and into the early hours of Saturday, targeting weapons warehouses and logistics support areas.
The group generally targets Egyptian security forces in northern Sinai but also claimed an attack on a tourist site in southern Sinai in April of a year ago.
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Twenty militants were arrested on Sunday by paramilitary Frontier Corps in an intelligence-based military operation in Pakistan's Balochistan province.
Relations between Egypt and Israel have improved dramatically since the army ousted Islamist Mohamed Morsi from the presidency in July, 2013.
The operation was launched as part of the efforts to reach the three-month deadline set by President Abdel-Fattah al-Sisi to eliminate terrorism after the mosque attack that killed 310 people in the northern Sinai city of Arish in November, 2017.
The head of the IS religious police in Sinai had previously said that Sufis who did not "repent" would be killed.
El-Sisi wrote on his official Facebook page that he was following the military operation to eradicate terrorism from Egypt with pride.