The attack, which took place overnight in the village of Al-Ayat about 50 kilometres from Cairo, left at least five others wounded, they said.
While the motivation was unclear officials suspect it was a criminal incident rather than terrorism.
State-run newspaper Akhbar al-Youm, citing witnesses, said two attackers arrived on a motorcycle and opened fire on people in the cafe before fleeing.
Security officials arrived at the scene and also interviewed injured people in hospital to try to identify and arrest the attackers, the newspaper reported.