According to the interior ministry, they also planned to target government and tourism sites, as well as army and police staff.
The news broke on Saturday hours after four people were killed when a bomb blast struck a tourist bus near the Giza Pyramids (pictures). Three Vietnamese tourists and their Egyptian guide died.
In a new statement, government officials said 40 militants died when security forces stormed hideouts in the Sinai Peninsula and the Greater Cairo area.
They reported that ten were killed during a raid in the coastal city of el-Arish in the unstable north of Sinai.
A further 14 died in a suburb of Cairo, while there were 16 more deaths in a housing project to the west of the capital.
For years, Egypt has been battling in the peninsula against an Islamic insurgency which has occasionally seen violence spill over onto the mainland - affecting Christians or tourists.
Attacks on believers - often targeting churches or buses travelling towards remote monasteries - have killed more than 100 people.
Associated Press said Friday's attack will prompt authorities to go further in tightening security around church buildings ahead of next month's Coptic Orthodox Church Christmas celebrations.
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