The assailants who were on a motorcycle shot randomly at the people as they left the church in north Cairo’s Al-Warak neighborhood on Sunday.
“There were two men on a motorbike and one of them opened fire,” the ministry said, adding that an eight-year-old girl, a woman and a man were killed and nine others wounded in the attack.
Meanwhile, security sources said that it is not clear if those who lost their lives were Christians.
An official from the Egyptian Health Ministry also confirmed the fatalities but said 12 people were wounded.
Ahmed al-Ansari added that four of the 12 were in a critical condition, noting the number of the injured could rise.
On Saturday, a car bomb went off near an Egyptian military intelligence building in the Suez Canal city of Ismailia, leaving at least six soldiers injured.
Egypt has been experiencing unrelenting violence since July 3, when the Egyptian army ousted Mohamed Morsi, the country’s first democratically-elected president, suspended the constitution and dissolved the parliament. The army also appointed the head of the Supreme Constitutional Court, Adly Mahmoud Mansour, as the new interim president.
Egypt’s military-installed interim government has launched a bloody crackdown on Morsi supporters and arrested more than 2,000 Muslim Brotherhood members, including the party’s leader, Mohamed Badie, who was detained on August 20.
About 1,000 people were killed in a week of violence between Morsi supporters and security forces after police dispersed their protest camps in a deadly operation on August 14.
Morsi and other Brotherhood leaders have accused the military of launching a coup that reversed the gains of the 2011 revolution against former dictator, Hosni Mubarak.