British Transport Police were called to the line just before 5pm and trains towards Huddersfield were hit by delays of nearly an hour.
Train passengers were informed by conductors that shots had been fired at a train between Mirfield and Dewsbury.
Yorkshire Post business reporter Ismail Mulla was on a train from Leeds to Dewsbury when an announcement was made.
He said: "I was catching the 17.18 from Leeds to Dewsbury. We got moved to a different platform before we left and it was late leaving Leeds.
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“About two minutes into the journey the conductor said they expect further delays getting to Dewsbury because there is somebody shooting at the trains between Mirfield and Dewsbury.
“The lady next to me turned round and said to me ‘Shooting? Really’.”
But it turned out that the trespasser on the line was just a fisherman.
A British Transport Police spokesman said today that the train driver had made the call in good faith.
He added: “At 4.52pm officers were called to the line close to Mirfield after a report of a man being in possession of an item thought to be a firearm.
“Following extensive enquiries, it appears this was a fishing rod, mistakenly thought to be a weapon. No further action was taken in relation.”
The resulting disruption had cleared by around 6.30pm last night.