Sixteen militants were killed and four arrested in a major security operation launched by Egypt on Friday, the Egyptian military said on Sunday, the first casualties in a campaign aimed at crushing insurgents behind a string of attacks.

The military also said in a statement carried by state television that 66 targets, arms depots and SUVs and motor-bikes used by militants were destroyed in raids focused mainly in Sinai, but also including parts of the Nile Delta and the western desert.

President Abdel Fattah al Sisi, who is seeking re-election in March, ordered the armed forces in November to defeat militants within three months after an attack on a mosque killed more than 300 people, the deadliest such incident in the Arab world's most populous country.

Insurgents have been targeting security forces since 2013 when the army, then led by Sisi as army chief, ousted democratically elected president Mohamed Morsi of the Muslim Brotherhood movement following mass protests against his rule.

The operation involves troops from the Egyptian air force, navy and ground forces as well as the police and border guards.

"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.

A total of 16 militants were killed, it said.

The statement also said forces involved in the operation found a media centre with computers, communication equipment and books and documents related to jihadi ideology.

Security forces also uncovered and destroyed six farms used to grow banned narcotics, the statement said.