The ministry said 13,162 people have been wounded in the Israeli strikes, which began on October 7.
Among those killed were 16 people who died at the compound of the Orthodox church of Saint Porphyrius in Gaza City late on Thursday, the ministry added.
The Hamas health ministry also said that since the conflict erupted, 46 medical personnel had been killed and 85 wounded in Gaza.
Twenty-one health facilities were out of service due to lack of fuel, it added.
A statement released by Caritas Internationalis, a Roman Catholic charity, said around 500 people took refuge at the church, including five members of the Caritas staff, along with their families.
"We were devastated to learn of the death of our colleague Viola, 26-year-old, who was killed alongside her husband and their infant daughter" in the strike, read the Caritas statement.
In addition to the deaths, other people are still under the rubble, the statement added.
Witnesses said the strike appeared to have been aimed at a target close to the church.
The Israeli Defense Forces said its fighter jets had struck a "command and control center" belonging to Hamas that was involved in firing rockets toward Israel.
"As a result of the strike a wall of a church in the area was damaged,” the Israeli forces said.
Palestinians in Gaza are still waiting for humanitarian aid to enter Gaza from Egypt through the Rafah crossing.
The war in Gaza began after Hamas militia carried out a deadly raid in southern Israel on October 7, which left over 1,400 people dead, most of them civilians.