The incident occurred at around 5pm on Sunday as the FC Zurich supporters were returning from a match at Sion in a special train, 20 Minutes reported online on Monday.
The culprits stopped the train at St. Saphorin, a community east of Lausanne, where the railway runs close to the Lake Geneva shoreline.
They forced the doors open and jumped into the lake, the newspaper reported.
The supporters also through objects at bathers on the beach, 20 Minutes said.
“I almost got a beer can in the face while were peacefully sitting on the beach,” one bather is quoted as saying.
“Other objects were also thrown in the lake.”
Around 50 supporters scaled a barrier along the rail tracks and crossed through a vineyard before dipping in the lake.
The emergency stop forced the delay of five trains on the line, according to SBB.
“For the moment the troublemakers have not been identified,” railway spokesperson Patricia Claivaz said.
Every year, vandalism costs SBB around three million francs.