The bomb targeted a truck distributing water to police checkpoints on a highway leading to El-Arish, the capital of north Sinai, the ministry said in a statement.
The explosion also wounded a police conscript, it added.
Jihadists have killed hundreds of soldiers and police since the military overthrew Islamist president Mohamed Morsi in 2013.
They pledged allegiance to IS more than a year later, and their attacks have persisted despite a sweeping military campaign in the peninsula which borders Israel and the Gaza Strip.