Only two passengers and two crew members were on the train when the accident occurred around 6:00 am (0500 GMT), BLS spokeswoman Stephanie Hofer told AFP.
The avalanche, which appeared to have been unleashed by unusually warm temperatures, did not hit the train but blocked the track near the scenic Goppenstein entrance to the Lötschberg tunnel in the southern canton of Valais.
"No one was injured," Hofer said, explaining that the train had struck the snow and jumped its track.
The people onboard had been evacuated but the train has not been moved due to the high risk of more avalanches in the area, she said.
The accident happened as temperatures across much of Switzerland rose sharply overnight, with meteorologists describing "exceptionally warm temperatures" in Valais and predicting the mercury there could reach 15 degrees Celsius (59 degrees Fahrenheit) by Monday.
"It is very dangerous when it is too warm," Hofer said, adding: "We think there will be more avalanches."
The rail connection between Goppenstein and Hohtenn would remain closed for the time being, and passengers would be transported by bus, BLS said.