Military vehicles rolled into the village on the edge of the capital just after dawn in search of "terrorists", a security official said.
"A heavy exchange of gunfire ensued between the security forces and the terrorists," killing Giza deputy security chief General Nabil Farrah, the official said.
Television footage showed thick teargas hanging over the rural patch near the Giza pyramids, as army and police vehicles moved around deserted parts of Kerdassah.
On August 14, just hours after authorities launched a crackdown on two protest camps in Cairo of supporters of ousted Islamist president Mohamed Morsi, 11 policemen were found dead at the Kerdassah police station.
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Several other police stations near the village were also torched.
Today's operation "is to clear the village of terrorist elements," the security official said.
The operation was launched after a 3:00 am meeting of interior ministry officials.
The operation in Kerdassah comes after a similar crackdown was launched in the town of Delga in central Egypt on Monday.
Meanwhile in Cairo, several metro lines serving hundreds of thousands of commuters were briefly grounded after two unexploded bombs were found on the tracks in a south Cairo station.
Bomb experts were dispatched to the scene and combed the tracks for more devices, one official said. Services resumed soon afterwards.
Egypt has been gripped by security related problems since the 2011 uprising that toppled longtime autocrat Hosni Mubarak.
The army has also been engaged in a campaign in the Sinai peninsula, pouring troops and armour to crush militancy which surged after the army overthrew Morsi.
The Islamist president's removal came after millions took to the streets to demand his overthrow after a year-long turbulent rule that deeply polarised Egyptians.