The report shows a £32bn (40bn) cost increase in the 30 schemes to £303bn (379bn). It calls on the EU to put in place "more frequent and regular updating of costs and monitoring of schedules" on the projects, which include the upgrade of the UK's West Coast Mainline.
"A poor project management structure is leading to a lack of planning and coordination, and a failure to identify problems and institute necessary design and programming changes," says the report.
It also claims that the drawing up of the 30 projects was done too quickly, without rigorous enough research into the cost and deliverability of the schemes, and before they had been fully committed to within the member country.
"When the list was drawn up, member states selected priority projects in a relative short period of time. This should have taken much longer to make a better estimate at the investment costs and define better the project scope."
Member states, including the UK, are also accused of not giving enough updates on the changing costs of schemes. "It should be a requirement that member states notify European institutions of revisions to costs frequently and regularly," says the report.
Freight Transport Association external affairs director Geoff Dossetter said any initiative to improve the reporting process would be welcome.