A Czech court has rejected a discrimination suit filed by a Somali refugee, who was banned from wearing her headscarf in a nursing school, the first case of its kind in the European Union state.

"The suit, which the plaintiff lodged seeking an apology and 60,000 crowns ($2,350) in compensation, was rejected," said Justice Daniela Cejkova, handing down the verdict in a Prague court on Friday.

Ayan Nuur filed a lawsuit against the school after she was not allowed to attend while wearing a headscarf.

The school argued that the young woman had never formally enrolled in the establishment. Ivanka Kohoutova, the school's principal, also argued that wearing a scarf covering the hair, ears and neck, and revealing only the face contravened its safety and hygiene standards.

Nuur, who was granted asylum in the Czech Republic in 2011, did not attend the trial, but was represented by her lawyer.

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During the trial, a group of female students came in support of the school and its rules against the head covering, reported the Czech news agency, CTK.

A group of Muslims also came out in support of Nuur, the agency said.

The Czech Republic is a secular country of 10.5 million people, with a Muslim community of only 10,000 to 20,000 members. It has no law covering the wearing of religious garments.

But like elsewhere in Europe, anti-Muslim sentiment has been on the rise there following the 2015 refugee and migrant crisis when more than one million people, mostly refugees fleeing violence in Afghanistan, Iraq and Syria, entered the EU.

Czech President Milos Zeman, known for his fiery anti-migrant rhetoric, insisted last year that it was "practically impossible" to integrate the Muslim community into European society.

Members of the public present in court on Friday sang the Czech national anthem and applauded after the verdict was handed down.