The military raid came a day after an explosion targeted two army armoured vehicles in Al-Arish city in North Sinai which killed seven Egyptian soldiers and injured four others seriously.
The army has destroyed 15 houses and shelters of the terrorists, security officials said.
North Sinai has witnessed many violent attacks by Islamist militants since the January 2011 revolution that toppled ex-president Hosni Mubarak.
Militant attacks targeting police and military increased after the ouster of Islamist ex-president Mohamed Morsi last year.
The military has launched security campaigns in the area, arrested suspects and demolished houses that belonged to terrorists, including those facilitating tunnels leading to the Gaza Strip.