Police in the canton of Nidwalden said that the foreign-registered minibus was hit by the train at a level crossing near the village of Wolfenschiessen.
The injured Israelis were taken to hospital by helicopter and ambulance.
The crash, which took place at 8:40 am (0640 GMT), involved a train operated by Zentralbahn, a company that provides local services in the mountainous region.
None of the train passengers were injured, police said, and the line was closed for over five hours.