The claim at the European Court of Human Rights in Strasbourg derives from debts that Croatian firms incurred at the now defunct Ljubljanska Banka (LB) before the two countries declared independence in 1991.
Slovenian Justice Minister Goran Klemencic told a news conference on Thursday that Croatian authorities prevented LB recouping the debt after the break-up of Yugoslavia.
The move follows a ruling of the same court last year which ordered Slovenia to repay depositors of the same bank in Croatia and Bosnia who lost their savings when Yugoslavia collapsed in 1991.
Although Slovenia had argued the issue should be settled as a part of succession talks of the former Yugoslav states it has already started repaying the depositors and expects to spend some 385 million euros on the repayments.
Slovenia and Croatia are the only former Yugoslav states to have joined the EU so far but have not yet managed to determine parts of sea and land border between themselves.
Reuters