The country’s interior ministry did not say whether the suspected militants were connected to the bombing on Friday.
Security forces killed 30 people during raids on their hideouts in Giza, where it said “terrorist elements” were planning a series of attacks targeting state institutions and the tourism industry.
Another 10 suspected miltants were killed in North Sinai, where the country is fighting an insurgency led by Islamic State.
According to state news agency MENA, the suspects were killed in a gun battle.
The ministry did not give any details about the suspects’ identity or whether there had been casualties or injuries among security forces.
Photos of the bloodied bodies with blurred faces were published by the ministry.
Three Vietnamese tourists and an Egyptian guide were killed when a roadside bomb hit their tour bus less than 4km (2.5 miles) from the pyramids in Giza.
Another 10 people were injured.
It was the first deadly attack against foreign tourists in more than a year, and came as the country’s tourism sector recovered from a sharp drop in visitor numbers in 2011.
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The group had been on the way to a sound and light show at the pyramids, which they had visited earlier in the day.
Le, 41, who was on the bus but not hurt, said: “We were going to the sound and light show and then suddenly we heard a bomb. It was terrible, people screaming.
“I don’t remember anything after.”
Vietnam condemned the attack, and called on Egypt to find those responsible. Egypt’s prime minister said the bus had taken a different route to the one which was secured by forces.
The government has said fighting Islamist militants is a priority, as it works to restore stability after years of turmoil following 2011’s Arab Spring protests.
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