"A number of policemen" were killed in the operation, said the Egyptian interior ministry but did not reveal the exact casualty figures from the confrontation.
The security sources put the death toll of policemen, including officers and conscripts, at over 50.
The sources said the suspected militants also used explosive devices in the attack. A fake claim in the name of the small extremist group Hasm, reported by multiple local media, spread on social media soon after the attack.
Hundreds of police and army personnel have been killed since then.
State television said Saturday a security alert was declared in the area to hunt down militants.
According to a statement released by the presidency, El-Sisi received during the meeting detailed reports on the incident.More news: Two federal judges halt Trump's third travel ban
The number of dead was expected to rise, the sources said.
Condemnations of the attack came in from the Middle East and Europe, with France -where Sisi is due to visit next week- pledging solidarity after the latest losses for Egypt's security force in "the fight against terrorism". The Muslim Brotherhood denies this.
Egypt has been battling an insurgency since 2013 when the military deposed Mohamed Morsi, Egypt's first freely elected president, in a coup.
Analysts say a section of the Brotherhood has encouraged armed assaults against the police.
No terrorist group claimed responsibility of the attack.
He also called on officials to exert all possible efforts to capture the terrorist elements involved in the shootout. The military has launched security campaigns in Egypt's restive North Sinai province, arrested suspects and demolished houses that belong to terrorists, including those facilitating tunnels leading to the Gaza Strip.