When the campaign started on Friday, the armed forces raided terrorist hideouts in North Sinai's cities of Arish, Rafah and Sheikh Zuweid while the police killed three militants in Cairo and arrested 14 suspects in several provinces.
Tamer el-Rifaai, security forces seized weapons, vehicles, communications equipment and other hardware used by the militants during the operation.
He gave the order in November after a gun and bomb attack on a mosque killed more than 300 people.
Apart from Sinai, the Egyptian army said the operation would also cover parts of the Nile Delta and the Western Desert, where other militants have waged attacks, some believed to be staged out of neighbouring Libya. He authorized chief of staff Mohamed Hegazy to use " brute force".
The military has also destroyed 66 targets, arms depots, 12 explosive devices and 11 SUVs used by terror elements, the source said.
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The operation was launched in the Sinai.
Naval units from a Mistral helicopter carrier have continued to comb the coast of Arish, the capital of North Sinai governorate, while police and coast guards intensified security measures and patrols, including in Egypt's southern desert and through mountainous paths along the southern and western borders, to "thwart any attempt to sneak through global borders".
In the first part of 2017 IS stepped up attacks against Christians in Sinai and elsewhere in Egypt, claiming two deadly attacks on churches in Tanta and Alexandria on 9 April.
In addition to its attacks on Christians, IS has adopted a threatening tone against Sufi Muslims, whom it considers to be heretics. A total of 16 militants were killed, it said. Locals said the mosque was popular among Sufis.