The man is likely to face charges of encroachment in a dangerous manner in rail traffic, the spokesman told German press agency DDP.
The damages from the collision on Saturday evening near the city of Fulda in the state of Hesse could reach into the millions of euros, according to German rail carrier Deutsche Bahn. Bahn officials said there was also another minor train collision with sheep earlier in the evening.
The prosecutor's office in Fulda will investigate whether the shepherd was negligent, DDP reported.
The crash occurred on Sunday as an ICE train from Hamburg entered the Landrücken tunnel while travelling at a speed of 200 kilometres an hour. It derailed after slamming into a flock of 40 sheep that had somehow wandered onto the tracks.
Ten of the train's 12 cars were thrown clear of the tracks, and the salvage operation is expected to last at least a week. Forty to 50 people are working on the recovery operation, the German newspaper Main-Post reported on its website on Monday, driving cranes into the tunnel from both directions.
German media also reported on Monday that one of the engineers charged with rescuing the stricken train's 135 passengers was drunk.
Police stopped the rescue train on its way back from the crash site near the city of Fulda in the state of Hesse so both engineers driving it could be given a field sobriety test, the Main-Post reported.
One of the engineers was drunk, German press agency DPA reported. Federal police are investigating whether the man was a hazard to rail traffic, spokesman Winfried Felbinger told DPA.
How much the man had been drinking and whether he was incapacitated was not yet clear, according to DPA. The rescue train was based in the city of Würzberg, in the German state of Bavaria.
The wreck is likely to cause delays of around 30 minutes on the rail routes between Hamburg and Fulda as well as Fulda and Munich.