The operation also freed a police officer who had been taken hostage in the October 20 shootout with militants in the Western Desert, a army official told AFP.
Authorities are fighting the Egyptian branch of the Islamic State group, which has killed hundreds of security personnel in northern Sinai, more than 500 kilometres (300 miles) from the site of this month's clash.
State television said Tuesday the military had acted on "confirmed information" on the whereabouts of the militants involved.
The raid destroyed three four-wheel-drive vehicles carrying large quantities of weapons, ammunition, and "extremely explosive material", it said.
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The military official told AFP that the operation, conducted in cooperation with the police and which used air strikes and ground forces, succeeded in freeing police captain Mohamed al-Hayes.
He had been kidnapped when armed extremists attacked a police convoy less than 200 kilometres southwest of Cairo, killing at least 16 policemen.
No group has yet claimed responsibility.