An estimated 40,000 have entered the country since Saturday.
The figure for Wednesday exceeds the peak recorded by Hungary on 23 September, when just over 10,000 refugees entered the country in a single day.
Between Saturday, when the latest refugee surge started, and 6 AM this morning about 34,000 refugees crossed into Slovenia. With the latest arrivals morning arrivals, the total has now risen to about 40,000.
When refugees started arriving over the weekend due to the closure of Hungary's border with Croatia, about 3,000 came per day.
The daily number rose to over 7,000 Monday and Tuesday, spiking at 12,600 yesterday, show statistics released on the Slovenian police website.
The vast majority of arrivals in the past two days came in the evening or during the night.
They are typically dropped off by Croatian authorities at several points close to the border in the evening and make their way across the border during the night.