Four train cars went off the rails on Wednesday morning near Kibbutz Kfar Menahem, in the South.
One person sustained light-moderate head injuries, two others were lightly hurt and some 20 people were treated for shock.
Several Magen David Adom ambulances were scrambled to the scene to treat the injured, as well as police units and inspectors from the Transportation Ministry.
Paramedics alerted hospitals in the area to be prepared to receive multiple patients from the incident, but retracted the alert within a few minutes.
Investigators believe that an object that was lying on the train track or that fell from the train itself caused the derailment.
The train had left Beersheba bound for Tel Aviv when it derailed near the kibbutz, next to Kiryat Gat. Israel Radio reported that the section of rail affected by the crash would be closed until Friday.
MDA emphasized that although the train cars went off the track, they did not overturn.