It has been alleged migrants and refugees are being held in the country for up to 90 days in what the UN human rights chief has called "degrading conditions".
It's a claim the Czech Government denies.
It comes as a constant flow of migrants continue to make their way to northern Europe.
It's a damning indictment of the Czech Republic's policy from the United Nations.
UN human rights chief Zeid Ra'ad al-Hussein has slammed the country's treatment of those seeking asylum.
He claims there have been major violations of human rights, with the detainment of people in detention centres in poor conditions for up to three months.
Czech authorities have also been accused of strip-searching people for money to pay for their own detention.
Mr Hussein's spokesman, Rupert Colville, says the violations are extremely alarming.
"There appears to be violations of human rights of the migrants and refugees, not isolated violations, not coincidental, but essentially systematic, and this is basically to do with the fact that they are being detained, pretty much as a matter of course, for 40 days in some cases, which is just about permissible under Czech law, but in other cases way beyond that, so even beyond what Czech legal system allows. They are not being, many of them are unable to challenge their detention legally."
While other European countries have implemented policies to restrict the flow of migrants, the Czech Republic opted instead to detain them.
The UN says some people who challenged their detention have been released, but most did not know their rights and were unable to exercise them.
Mr Colville says that's partly because their mobile phones were taken away.
He says children are also being held in centres.
"The rights of the children are being clearly systematically violated. Children should never be in detention solely because of their migration status or the migration status of their parents; that is never in their best interest, it's a violation and its never justifiable."
The Czech government is strongly denying the allegations.
It says the detentions are legal and work is being continuously done to improve conditions in the centres.
The Czech Republic lies to the north of the main migration routes taking refugees through the Balkans to Germany.
It has seen only a fraction of the hundreds of thousands passing through Hungary and Austria.
But with Hungary closing its border with Croatia last week, migrants are now being forced to take different routes.
That's caused an influx to make their way into Slovenia.
Slovenian interior minister Vesna Gyorkos Znidar has asked the European Union migration commissioner for help dealing with the flood of people.
"We have briefed the commissioner about the situation in the country. A total of 43,000 migrants arrived in Slovenia in the past five days and only over the past 24 hours there were 12,600. We have also informed the commissioner about the way Croatia is handling this and that Croatia's refusal to cooperate is causing huge problems for us."
European Migration Commissioner Dimitris Avrampoloulos says the EU is at the ready.
"We are standing by Slovenia during this difficult moment. Slovenia is not alone and we are ready to assist the country, both technically and financially."
Slovenia says it would be able to accept up to 2,500 refugees per day, as long as Austria and Germany did not strengthen their border controls.
Its parliament has also passed legislation giving the army more power to help guard its border.
But Syrian refugee Sunami says most migrants are just happy to have escaped the warzone, and will settle in any European country that will take them.
"Any safe place that will treat us like a human because we fled from our country because they treated us like animals, there is no value for the human in the Syria, as you see. It was a catastrophic journey, actually. And now, we will continue."
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