European Court of Auditors report concluded approximately EUR 2.35 billion (US$ 2.65 billion) in cost overruns for the Rail Baltica project. Initially, the project was planned to have expenses of EUR 4.64 billion (US$ 5.23 billion) or allocated EUR 5.8 billion (US$ 6.54 billion), but now the project is expected to cost EUR 7 billion (US$ 7.90 billion). The risk of even more increment in cost is present. 

The Rail Baltica network, a high-speed line of 870 kilometers of double track and standard gauge, will quickly, sustainably and securely connect the capitals of Estonia, Latvia, and Lithuania and offer a direct connection to the rest of Europe, without requiring adaptations. Currently, the Baltic States have different track gauges than the rest of Europe, so until the new line is available it is necessary to adapt widths or change vehicles, with the costs that this entails in terms of time and money. For this reason, most of the goods traffic and rail services in the Baltic States is with the countries of the Commonwealth of Independent States (CIS), mainly Russia, instead of the rest of the EU through Poland, something which the new rail infrastructure will foreseeably improve on.

The auditor report also states the uncertainty of economic longevity as the traffic headed North-South is not significant, and most freight is carried by land or by sea. The project is also prone to extend the deadlines for the works. A mixed-type passenger-freight transport line is required to make the project economically feasible.