The militants opened fire on the police as they approached the hideout in Dairut, a town in the southern province of Assiut, the interior ministry said in a statement on its Facebook page.
The police were acting on intelligence that "a group of terrorists who adhere to the beliefs of the Islamic State group were hiding in a residential apartment in uninhabited buildings", it said.
When the six militants opened fire, the police shot back and killed them.
The police found a bomb, five automatic weapons, ammunition, military uniforms, and "educational publications containing the concepts and slogans of the (IS) group," it added.
IS has been leading a deadly insurgency that has killed hundreds of policemen and soldiers since the army overthrew Islamist president Mohamed Morsi in 2013 and cracked down on his supporters.
While IS has been operating mainly in North Sinai, they have also carried out attacks in other parts of the country, including Cairo.
Groups other than IS have also carried out attacks in Egypt targeting policemen and judges.
Gunmen on Friday shot dead a National Security Service officer as he was leaving his home north of Cairo.
The militant group Hasam claimed responsibility.
On Saturday, the interior ministry said police killed two senior Hasam members in a shootout near Cairo.
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