Mantas Dubauskas, spokesman for the state railway company, said that a provisional payment had been made, which means that the money or part of it would be returned if the EU's court annulled or reduced the fine.
Lietuvos Geležinkeliai paid the fine from its accumulated reserve without using a bank guarantee. The company intends to ask the European Commission for immunity from the fine or a reduction. It has until early April to do so.
The railway operator in mid-December filed an appeal to the EU's General Court in Luxembourg over the fine.
It also plans to rebuild the 19-kilometer rail track from the Orlen Lietuva crude refinery in Mažeikiai, in northern Lithuania, to Renge in Latvia, which was removed back in 2008.