A police spokesman says the accident near Neuhausen station occurred shortly after 7.30 a.m. local time.
Nine of the injured people were taken to nearby hospitals; the spokesman didn't have details on the injuries but said none of their lives were believed to be in danger.
It wasn't immediately clear what caused the collision. A locomotive for one of the trains - a double-decker passenger train - derailed.
Rail traffic in two directions from Schaffhausen, a town on Switzerland's northern border with Germany, was interrupted and buses were being used instead.
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