Over two days, the Egyptian Armed Forces have killed 16 militants and arrested four others, said al-Rifai in a statement on Sunday.
El-Sissi, who has waged one of the most sweeping crackdowns on dissent in Egypt's modern history, says he is the only one who can restore Egypt's security, and ordered the Sinai operation after militants struck.
A video recording posted on social media, purportedly from a group affiliated to Islamic State, appeared to showed masked militants executing soldiers and civilians they accused of collaborating with security forces.
Egypt launched a "comprehensive" security operation involving the country's army, navy and air force, aimed at pushing armed groups out of the Sinai Peninsula, parts of the Nile Delta and the Western Delta on Friday.
"The air force targeted and destroyed 66 targets used by terrorist elements to hide from air and artillery attacks, and to escape from their bases during raids", the statement said.More news: SC to resume final hearings in Ram Janmabhoomi-Babri case today
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The air force also discovered and destroyed an explosives-making laboratory and a communications centre, as well as six cannabis and opium fields, he said. The Sinai borders Israel and the Gaza Strip and has always been a bastion for Islamic insurgent groups tied to al-Qaida.
Egypt denied this, and Israel declined to comment.
Last week the New York Times reported that unmarked Israeli aircraft were carrying out covert strikes in Egypt with the Egyptian president's approval.
At least 10 terrorists have been killed on Sunday during a police raid in Arish city of Egypt's North Sinai province bordering Israel and the Palestinian Gaza Strip, a security source and medics told Xinhua. They are blamed for a series of bomb, gun and suicide attacks that have killed hundreds in Egypt. No group has yet claimed responsibility for the mosque attack though.
The attacks, mainly targeting police and military, increased after the ouster of Islamist ex-president Mohamed Morsi in 2013 by military following massive protests against his rule. Last year, militants attacked a Sufi mosque in the region, killing 311 worshipers.