The president of the Czech Republic has rejected accusations from the UN’s human rights chief that his country is committing systematic rights violations through its policy on refugees.

Zeid Ra’ad al-Hussein said on Thursday the EU member state’s policy of detaining refugees for up to 90 days and strip-searching them for money to pay for their own detention amounted to human rights violations.

He also said he was alarmed by a xenophobic public discourse, including Islamophobic statements by Miloš Zeman, the Czech president, and concerned about the conditions in detention facilities. Children were also being detained, which was unjustifiable, he said.

But Zeman’s spokesman said the president rejected the criticism: “The president has long warned of the threat of Islamic fundamentalism. He stands by his opinion and he will not change it under pressure from abroad.”

Europe is struggling to deal with its biggest refugee crisis since the second world war as the conflict in Syria among others prompts millions to leave their homes. On Thursday the Slovenian authorities said more than 12,000 migrants had crossed into the country in the past 24 hours, with thousands more expected. They asked the rest of the EU for help in dealing with the influx of people.