The desperate refugees and migrants were forced to spend the night in freezing temperatures near rail tracks after police stopped them from walking across the border dividing the two EU states.
They are among thousands of people -- mostly fleeing violence in Syria, Iraq and Afghanistan -- who forged a new route to northern Europe after Hungary sealed its Croatian border with a razor-wire fence.
A train carrying around 1,800 people arrived overnight at the Sredisce ob Dravi checkpoint on the Croatian side, but only 500 of "the most vulnerable" were allowed into Slovenia and taken to a nearby registration centre, police spokesman Bojan Kitel said.
"We try to carry out a coordinated and manageable inflow to avoid exceeding the accommodation capacity we have in Slovenia. For that reason, we do not let in migrants from Croatia without first having the capacity. We give priority to the most vulnerable categories," he told AFP.
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Long lines have also formed on Croatia's border with Serbia. Several hundred people remained stuck there on Monday morning, after having spent the night in rain and cold weather, an AFP photographer said.
Slovenia stressed Sunday it would remain firm in its decision to handle up to 2,500 migrants a day -- half the amount demanded by Croatia -- to help ease pressure on both its own and Austria's borders.
Interior ministry spokesman Bostjan Sefic said Austrian authorities had told Ljubljana they couldn't handle more than 1,500 new arrivals a day.
"There are no restrictions in place," interior ministry spokesman Karl-Heinz Grundboeck told AFP on Monday.
Some 2,600 migrants entered Austria from Slovenia this weekend, police figures show.
Meanwhile no new crossings have been reported near the Hungarian border, from where thousands of people poured into the Alpine nation in August and September.