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A horrified passenger saw a pigeon fall from the sky after train bosses ordered a cull.
Southeastern commuters heard loud bangs as they waited for their trains.
Then, at least one passenger saw a pigeon plummet to the ground on the opposite platform.
Now rail chiefs have admitted they should have carried out the shooting when there was no-one was around, and they are now reviewing their policy.
The birds were shot at Dover Priory Station, while passengers waited for their trains.
One of those who witnessed the pigeons being shot was Andy Chandler, who said he heard a couple of loud bangs as he waited for a late Deal train. He then saw a pigeon fall to the ground on the opposite platform.
He said he was told men from a pest control company were shooting all the pigeons.
"I am not anti-hunting, or very fond of pigeons, but I was alarmed to find that the pest control company were using some sort of rifle and shooting while passengers were waiting on the platforms," he said.
A spokesman for Southeastern said the station had a problem with feral pigeons fouling on the platforms, but the cull should have been carried out when there was no-one there.
A statement added: "A professional pest control company has been contracted to deal with the issue and install netting at the station to prevent feral pigeons from roosting in the platform canopies.
"Although every attempt is first made to shoo feral pigeons away, it is sometimes necessary to humanely cull persistent feral pigeons to prevent them becoming trapped in the netting.
"A careful check is always made to first remove the occasional nest, eggs or chicks which are humanely dispatched.
"In this case a cull was necessary after a pigeon became trapped. The contractor had advised Kent Police of the operation.
"The contractor was of the understanding that the station was clear of passengers. The timing of the cull was supposed to occur following the last train of the evening.
"It is unfortunate that in this case a member of the public witnessed this activity and we’ll be reviewing the matter with the contractor to ensure this doesn’t happen again.
"All works are carried out under authorised method statements and risk assessments."
The spokesman said the firm involved was only shooting one pigeon which was caught in the netting and that there were very few passengers – possibly only one – on the station at the time.