Wales does not get its "fair share of rail funding" and the system must be "fixed", said a former Labour minister responsible for transport.
Plans for a £6.6bn Oxford-Cambridge rail line were previously classified as an England-only project, which means Wales could have been entitled to more money.
But the Treasury announced there was a "publishing error" in a 2020 document and it should have been classified as an England and Wales project.
Lee Waters, the Labour MS for Llanelli said the "cock-up" highlights the broader issue of how "unclear" and in need of reform the funding system is.