But it said that seven people, including an auxiliary policeman, had been killed and four injured as the gunman opened fire at the church.
The attacker also had an explosive device, a machine gun and 150 rounds, it added.
The ministry suggested he was known to security services, saying he was "one of the most active terrorist elements and he carried out several terrorist attacks which resulted in the martyrdom of a number of policemen and civilians".
However, the interior ministry account contradicts earlier ones from officials and witnesses, who spoke of a higher death toll and more than one attacker.
Video footage has also emerged appearing to show one gunman lying dead at the scene and another alleged attacker fleeing in a red car.
String of attacks
In the wake of Friday's attacks, President Abdul Fattah al-Sisi offered condolences to family members and vowed to continue "cleansing the country of terrorism and extremism".
Egypt's Copts have in the past accused the authorities of making only token gestures to protect them and these incidents will not help calm tensions, our correspondent Radwa Gamal says. Sky more