The train company is introducing a new express service from Cardiff to Holyhead every morning, which will affect a number of smaller stations in Shropshire.
It will only stop at a small number of stations - leave out Craven Arms, Church Stretton, Chirk and Gobowen.
The proposal was widely condemned by passengers, the Rail Users Group and the Chester Shrewsbury Rail Partnership.
Some 2,000 people signed a petition urging Transport for Wales (TfW) to reverse the decision.
However, councillor David Bithell, chairman of the Chester Shrewsbury Rail Partnership, has now received a letter from the Minister for Economy and Transport, Ken Skates, confirming TfW intents to press ahead and deliver the express service.
“As a partnership, we work well with all our members who represent the local authorities and residents and passengers of the entire line of route,” said Councillor Bithell.
“In welcoming Transport for Wales, to the Partnership when the Arriva franchise ceased, we were promised new and improved rolling stock and a future half hourly service.
“We pressed for sight of the draft timetable for many months with indications there would be no changes.
"It was extremely frustrating to learn they had implemented these changes with no consultation whatsoever and despite much representation to the minister, a petition and a report from the Rail User Group on the impact on current passengers, they have decided to implement the changes.
“Feedback to us indicates that passenger confidence in Transport for Wales is at an all-time low and rail users cannot understand that far from being focused on the passenger it seems they prefer to prioritise a franchise commitment in the express service above the needs of current passengers.”
He said the group will continue to press for the reinstatement of the lost services and will be involved in future discussions.
TfW said there would be visible improvements across the Wales and Borders network in the coming years.
These improvements will include additional weekend services for Craven Arms, Church Stretton, Chirk and Gobowen, from December 2022, the company said.