A ministry statement said police were still identifying the suspected militants killed in the raid in Ismailiya province after they opened fire on security forces approaching the hideout.
Militants carried out a bomb and gun assault on a mosque in Rawda village in North Sinai province on Friday, killing 305 people -- the deadliest in Egypt's recent history -- in an attack thought to have been carried out by the Islamic State group.
It is widely believed in Egypt that the massacre took place at the mosque because Sufi Muslims worshipped there.
The raid on the hideout was part of a security campaign in the province of Ismailiya around the Suez Canal separating the Sinai Peninsula from the rest of the country, and in the Nile Delta province of Sharqiya.
Police were pursuing leaders of "terrorist groups in North Sinai that aimed to carry out a series of hostile operations targeting important and vital buildings and Christian churches," the statement said.
Security forces were able to identify "a group of these elements and the hideouts they were using to hide, train, and store means of logistic support ahead of smuggling them to terrorist groups in North Sinai".
The statement said police also arrested six suspected militants and three people thought to have smuggled communications equipment to them.
It said weapons, ammunition and communication devices were recovered.
In the Rawda attack, authorities said up to 30 militants in camouflage and flying the black banner of IS surrounded the mosque and massacred worshippers during weekly Friday prayers.
Another 128 people were wounded.
Egypt's North Sinai-based IS branch has killed hundreds of policemen and soldiers, as well as civilians accused of working with the authorities, since the July 2013 ouster of Islamist president Mohamed Morsi.
The jihadist group has also targeted Sufis and Christians since authorities cracked down on Morsi supporters, killing more than 700 in one August day in 2013 as they cleared a protest camp in the capital.
President Abdel Fattah al-Sisi declared three days of mourning and vowed to "respond with brutal force" to Friday's killings, among the deadliest in the world since the September 11, 2001 attacks on the United States.
The army said warplanes struck militant hideouts in the North Sinai in retaliation.
Egyptian security forces killed 11 suspected "terrorist elements" during a raid on a hideout for militants providing support for jihadists in the northern Sinai, the interior ministry said on Tuesday.
