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"A number of passengers were concerned for the welfare of the snake and contacted police," the post said.
Police caught up with the man at Woy Woy Railway Station and determined he did not have a permit for the python, named Bread.
The snake was confiscated and taken to Woy Woy Police Station before being transferred to the Australian Reptile Park, where it was found to be in good health.
Police said the owner is expected to be charged with possessing and displaying protected fauna, which carries a maximum fine of about $225.
"If you put yourself in the shoes of someone who has a fear of snakes, that would be a terrifying situation," police Superintendent Danny Sullivan told the Australian Broadcasting Corp. "If I could give one piece of advice -- don't get your snake out on a train."
NSW Police joked about the incident on Twitter: "Dear Pokemon Go fans -- we can confirm it was NOT Ekans."