Some 2,700 refugees crossed into Slovenia from Croatia on Saturday, local media reported.
Overnight, Hungary closed its border with Croatia as migrants from the Middle East and Africa continued to flood the country trying to reach more affluent European nations.
According to the SEEbiz.eu news portal, the first flow of refugees, about 600, arrived by bus to the border crossings of Gruskovje and Petisovci.
Ljubljana is now in danger of being overwhelmed by migrants as Croatia plans to direct them to Slovenia now that the border with Hungary is closed.
On Friday evening, Slovenia was forced to stop rail transport from Croatia and strengthen security at its frontiers.