'Veganuary' adverts were placed on 20 Arriva buses in the county, paid for by the Shropshire Veggies and Vegans group.
They were designed by the national Veganuary campaign, which encourages people to go without animal products for the first month of the year.
It is the second year in a row that a row has broken out over the adverts, but the first time they have been removed due to the complaints.
One of the adverts focused on environmental side of veganism, while another was about the treatment of cows in the dairy industry.
Michelle D'Arcy-Jewell, who runs Shropshire Veggies and Vegans, said the group was shocked to be told by Arriva that the adverts would be pulled with no further discussion.
She said: "They did not say how many complaints there had been or who from.
"It is no different than me seeing a meat advert on the back of a bus. You just think, 'that doesn't apply to me'. If you don't want to look at it, then just don't.
"I don't know why the bus company has such a problem with it. I feel like it is totally unjustified.
"We know it is a farming community and we don't want farmers to go out of business, we just want them to farm differently.
"One of the adverts in particular was talking about the environmental impact of going vegan and I think that is a really important message to get out there.
"The adverts were not misleading at all, they were factually accurate."
An email sent to the group from Arriva said: "I have received a note from our franchise team that there have been numerous complaints to Arriva from the general public in regards to the content of your bus rear ads within Telford and Shrewsbury.
"We have taken the decision that they are to be removed from display due to these complaints."
Decision 'down to third party'
However an Arriva spokeswoman blamed an error in signing off the adverts and denied the decision was because of the content of the posters.
The company said the group would be reimbursed for the cost of the advertising, but Michelle said this was unsatisfactory as people had made donations specifically towards the campaign.
The spokeswoman said: "Advertising on our buses is managed by a third-party company where an approval process is in place.
"A recent customer complaint brought it to our attention that our agreed sign-off process with this third-party had not been followed on this occasion.
"We can confirm that the adverts have subsequently been removed.
"Arriva is and continues to be impartial and the decision to remove these adverts does not relate to the content, but was taken as the agreed procedure was not adhered to.
"We have taken steps to review our approval process with the third-party and are working with them closely on this matter."
The national Veganuary campaign responded to the decision, saying: "It’s outrageous these ads have been pulled when the messages are indisputable facts.
"Nearly every day scientists issue new warnings about animal agriculture’s heavy environmental toll and urge us to eat less meat.
"And every dairy farmer knows that cows, like all mammals, must have a baby in order to produce milk and it is standard practice to separate the calf from the mother within 24 hours.
"People have a right to know this and decide if it is something they are happy to support.”
Last winter Shropshire Council’s deputy leader Steve Charmley criticised Arriva for running the adverts in a county with so many livestock and dairy farms.