The security sweep comes as the country prepares for polls.
The Egyptian army announced the launch on Friday of a major operation against jihadists across swathes of territory including the Sinai Peninsula, heart of a persistent Islamic State group insurgency.
Police and troops have been put on "maximum alert" for the duration of Operation Sinai 2018, which also involves the airforce and navy, the army said in a statement.
Warplanes will bomb areas where jihadists are hiding while troops, tanks and armoured vehicles will be deployed on the ground, security sources said.
The security sweep in the Sinai, the Nile Delta and the Western Desert near the Libyan border comes as the country prepares for polls next month at which President Abdel Fattah al-Sisi is seeking re-election.
Egypt has been under a state of emergency since April last year, after two suicide bombings at churches claimed by IS killed at least 45 people in the cities of Tanta and Alexandria.
The goal of Operation Sinai 2018 is to tighten control of border districts and "clean up areas where there are terrorist hotbeds", army spokesman Tamer al-Rifai said in a televised address.
In a later update, he said the air force had targeted a number of homes and hideouts in the north and west of the Sinai.
The navy was boosting security at maritime borders "to cut off the influx of terrorists," he added.
Security sources and eyewitnesses confirmed that the operation was under way in the Nile Delta and North Sinai province.
Churches, tourists attacked
The security forces have been increasingly targeted by jihadists since the army overthrew Islamist president Mohamed Morsi in 2013.
Most of the violence has been in North Sinai province, but there have also been attacks on the military, police and even churches elsewhere, including Cairo.
Jihadists have also attacked tourists, killing all 224 on board a Russian plane carrying holidaymakers in 2015.
In November, Sisi ordered the armed forces chief of staff to restore security in Sinai within three months after militants killed more than 300 worshippers at a mosque.
Sisi, who is expected to easily win another four-year term next month after several potential challengers were either hobbled or dropped out, said on Facebook he was "proudly following the heroism" of the security forces.
Egypt has previously announced several major offensives to tackle the jihadist threat.
It also carried out air strikes against IS in Libya in 2015 after a video was released showing the beheading of 21 Christians, almost all Egyptian Copts, on a Libyan beach.
The military has boosted its operations on the border with Libya and repeatedly expressed concern about militants crossing over from the chaos-wracked country to launch attacks.