Rubesa said that with Brexit on the horizon, the European Union is about to move into a new era of how it funds its projects. "Assuming that Brexit is going to happen, I think all bets are off for business as usual in the EU, so we are working hard to make sure we are able to retain our priority project status," Rubesa told Euronews. "The three Baltic countries — Estonia, Latvia and Lithuania — on their own just cannot afford something like this."

Though Rubesa considers it "extremely likely" that Rail Baltica will retain its status as an EU priority project and that EU funding for it will be granted, the question is how much the project will eventually receive at a time.

Other challenges apart from funding include the alignment and cooperation between the Baltic states on the project as well as local environmental concerns, such as creating wildlife crossings in Estonia, Rubesa said.

She added that construction is still expected to begin in 2020.

The EU has committed itself to €1.2 billion in support of the project in the Baltic states between 2014 and 2020. Some €110 million were granted additionally. The project is estimated to cost a total of €5.8 billion under preliminary terms. The project is expected to be completed by 2026.