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.
It added that police had seized bomb-making materials, ammunition and a large number of weapons during the raids.
"A group of terrorists were planning to carry out a series of aggressive attacks targeting state institutions, particularly economic ones, as well as tourism. and Christian places of worship", the ministry statement said.
The bus was carrying 14 Vietnamese tourists and two Egyptians. Authorities said earlier the wounded include 10 Vietnamese tourists and the Egyptian bus driver.
Egypt's interior ministry has said at least 40 fighters have been killed on Saturday in response to an attack on a tourist bus in which four people killed the night before.
It occurred as Egypt's vital tourism industry is showing signs of recovery after years because of the political turmoil and violence that followed a 2011 uprising that toppled former leader Hosni Mubarak.
Two German tourists were stabbed to death at a hotel in the popular Red Sea resort of Hurghada a year ago.
The Interior Ministry said that "this comes as a continuation of the ministry's efforts in chasing terrorist elements involved in the implementation of hostile operations seeking to destabilize the country's security". No militant group immediately claimed responsibility for the attack.
The pyramids are one of the world's major tourist attractions, drawing nearly 15 million visitors every year.
Still, Egypt had 8.3 million visitors in 2017, according to BBC.
Egypt has for years been battling an insurgency in North Sinai, which surged following the 2013 military ouster of president Mohamed Morsi.
The army says that hundreds of suspected jihadists have been killed since the campaign was launched.