The ministry said the suspects were killed in gunbattles, but did not elaborate on the suspects’ identity or whether there had been any casualties or injuries among the security forces.
Weapons and explosives were found at the scene of the shootouts, the ministry said.
At least 17 people have been killed in an explosion targeted at a tourist bus in Egypt on Sunday.
The incident occured near the Grand Egyptian Museum, next to the pyramids of Giza.
South African and Egyptian tourist were among the injured in the attack, according to security and medical sources.
The attack comes just over a month before the start of the African Cup of Nations in Egypt from 21 June to 20 July.
The tourism industry, crucial to the Egyptian economy, has been severely affected by political instability and attacks following the 2011 revolt that led to the fall of President Hosni Mubarak after 30 years in power.
From 14.7 million in 2010, the number of visitors fell to 8.3 million in 2017.