They torched the tents at the camp in Brezice to protest at the slow process of registering them and moving them to the Austrian border, witnesses said.
They have also complained of a lack of food, water and blankets in the camp.
Meanwhile the Greek coastguard is searching for a migrant boat believed to have capsized with 14 on board near the island of Samos amid heavy rain.
Samos, where 69,000 people have arrived over the past year, is receiving the highest numbers of migrants of any Greek island apart from Lesbos.
Thousands of migrants continue to pour through the western Balkans and the leaders of those countries have been summoned to a special EU meeting.
The European Commission said President Jean-Claude Juncker had called Sunday's meeting because "there is a need for much greater cooperation, more extensive consultation and immediate operational action" to deal with what it called "the unfolding emergency".
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Last week Hungary closed its border with Croatia and Serbia and refused to let any more migrants cross, citing security concerns. As a result, the migrants have been diverted to Slovenia on their way to western Europe.
Slovenia says it has been overwhelmed by the nearly 20,000 migrants that have arrived since Friday. It had said it could only take 2,500 migrants a day.
The Slovenian army and the police are working to manage the flow, but aid agencies have been warning of dire conditions as bottlenecks develop at border crossings along the route, just as temperatures are beginning to drop.
But there is no sign that the numbers of migrants and refugees is slowing.
A number of boats carrying around 140 people, including children, arrived at the RAF base at Akrotiri in Cyprus on Wednesday morning.
Many of the migrants heading through the Western Balkans are trying to reach Germany, which is predicting an influx of at least 800,000 asylum seekers this year. Some estimates put the number at over a million.
Many of those will have their asylum bids rejected and a government spokesman confirmed on Wednesday that it was considering the use of military planes to help speed up the deportation process.
Defence Minister Ursula von der Leyen said army transport planes would be used, but only if civilian aircraft were not available.
Chancellor Angela Merkel's domestic popularity has declined in recent weeks because of the influx into Germany.
And an opinion poll on Wednesday said the proportion of Germans who were extremely worried by the situation had risen from 40% in August to 54%.
However a separate poll of members of Mrs Merkel's conservative CDU party found that 82% were happy with her as their leader.
A note on terminology: The BBC uses the term migrant to refer to all people on the move who have yet to complete the legal process of claiming asylum. This group includes people fleeing war-torn countries such as Syria, who are likely to be granted refugee status, as well as people who are seeking jobs and better lives, who governments are likely to rule are economic migrants.
Tents have been torched at a transit camp in Slovenia, allegedly by migrants angry at how they are being treated.