The incident took place at an unauthorised railway crossing on the Cairo-Ismaila desert road, they said.
Hossam Abdel Ghafar, the spokesperson of the Ministry of Health, said that at least seven people were killed and 25 others were injured when the speeding bus was hit by an oncoming train.
He said five of those killed were school children.
"Seven of the injured including three children are under intensive care as they are in a critical condition," Abdel Ghafar added.
Egypt has one of the world's highest accident rates owing to careless driving and poor road and vehicle conditions, which lead to thousands of deaths and injuries every year.
The WHO ranks Egypt as the world's tenth worst country in road accidents, after India, China and the US.
A recent report by the Central Agency for Public Mobilisation and Statistics (CAPMAS) said there were 15,578 car accidents in Egypt in 2013, up 0.4 per cent from the year before, which claimed the lives of 6,716 people and injured 22,411 others.
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