A four-year-old refugee has allegedly been raped by an Afghan man at a shelter for asylum seekers in Germany.

The Iraqi boy was living with his family among 600 other migrants at the centre in Boostedt, north of Hamburg, when he was assaulted.

His father told Kiel District Court his eight-year-old son raised the alarm on 29 March, saying his younger brother was in the toilet with a stranger.

When the man arrived he could see his son’s shoes next to those of an adult, shouting and trying to open the door before it was opened from the inside.

Number of child refugees crossing into Europe swells

He found his son and an old man with their trousers down, the Schleswig-Holsteinische Zeitungsverlag newspaper reported.

The father told the court he asked the man what he was doing with the boy, and was told he had been helping him go to the toilet.

“In that moment I believed him, I even thanked him in Persian,” he said.

The four-year-old later told his parents he had been forced to perform oral sex on the man – an allegation prosecutors have supported with DNA evidence.

Police said the 22-year-old suspect was immediately arrested on suspicion of aggravated sexual abuse of child.

He denies the allegation, while another Afghan man, 29, denies threatening the victim’s brother with a knife when he tried to stop the attack.

Both defendants remain in custody as the trial continues, with a verdict expected in October.

Refugees settle in Germany Show all 12 1 /12 Refugees settle in Germany Refugees settle in Germany Germany Mohamed Zayat, a refugee from Syria, plays with his daughter Ranim, who is nearly 3, in the one room they and Mohamed's wife Laloosh call home at an asylum-seekers' shelter in Vossberg village on October 9, 2015 in Letschin, Germany. The Zayats arrived approximately two months ago after trekking through Turkey, Greece and the Balkans and are now waiting for local authorities to process their asylum application, after which they will be allowed to live independently and settle elsewhere in Germany. Approximately 60 asylum-seekers, mostly from Syria, Chechnya and Somalia, live at the Vossberg shelter, which is run by the Arbeiter-Samariter Bund (ASB) charity 2015 Getty Images Refugees settle in Germany Germany A refugee child Amnat Musayeva points to a star with her photo and name that decorates the door to her classroom as teacher Martina Fischer looks on at the local kindergarten Amnat and her siblings attend on October 9, 2015 in Letschin, Germany. The children live with their family at an asylum-seekers' shelter in nearby Vossberg village and are waiting for local authorities to process their asylum applications. Approximately 60 asylum-seekers, mostly from Syria, Chechnya and Somalia, live at the Vossberg shelter, which is run by the Arbeiter-Samariter Bund (ASB) charity Getty Images Refugees settle in Germany Germany Kurdish Syrian asylum-applicant Mohamed Ali Hussein (R), 19, and fellow applicant Autur, from Latvia, load benches onto a truckbed while performing community service, for which they receive a small allowance, in Wilhelmsaue village on October 9, 2015 near Letschin, Germany. Mohamed and Autur live at an asylum-applicants' shelter in nearby Vossberg village. Approximately 60 asylum-seekers, mostly from Syria, Chechnya and Somalia, live at the Vossberg shelter, which is run by the Arbeiter-Samariter Bund (ASB) charity Getty Images Refugees settle in Germany Germany Mohamed Ali Hussein ((L), 19, and his cousin Sinjar Hussein, 34, sweep leaves at a cemetery in Gieshof village, for which they receive a small allowance, near Letschin Getty Images Refugees settle in Germany Germany Mohamed Zayat, a refugee from Syria, looks among donated clothing in the basement of the asylum-seekers' shelter that is home to Mohamed, his wife Laloosh and their daughter Ranim as residents' laundry dries behind in Vossberg village on October 9, 2015 in Letschin, Germany. The Zayats arrived approximately two months ago after trekking through Turkey, Greece and the Balkans and are now waiting for local authorities to process their asylum application, after which they will be allowed to live independently and settle elsewhere in Germany Getty Images Refugees settle in Germany Germany Asya Sugaipova (L), Mohza Mukayeva and Khadra Zhukova prepare food in the communal kitchen at the asylum-seekers' shelter that is their home in Vossberg village in Letschin Getty Images Refugees settle in Germany Germany Efrah Abdullahi Ahmed looks down from the communal kitchen window at her daughter Sumaya, 10, who had just returned from school, at the asylum-seekers' shelter that is their home in Vossberg Getty Images Refugees settle in Germany Germany Asylum-applicants, including Syrians Mohamed Ali Hussein (C-R, in black jacket) and Fadi Almasalmeh (C), return from grocery shopping with other refugees to the asylum-applicants' shelter that is their home in Vossberg village in Letschin Getty Images Refugees settle in Germany Germany Mohamed Zayat (2nd from L), a refugee from Syria, smokes a cigarette after shopping for groceries with his daughter Ranim, who is nearly 3, and fellow-Syrian refugees Mohamed Ali Hussein (C) and Fadi Almasalmeh (L) at a local supermarket on October 9, 2015 in Letschin, Germany. All of them live at an asylum-seekers' shelter in nearby Vossberg village and are waiting for local authorities to process their asylum applications, after which they will be allowed to live independently and settle elsewhere in Germany 2015 Getty Images Refugees settle in Germany Germany Kurdish Syrian refugees Leila, 9, carries her sister Avin, 1, in the backyard at the asylum-seekers' shelter that is home to them and their family in Vossberg village in Letschin Getty Images Refugees settle in Germany Germany Somali refugees and husband and wife Said Ahmed Gure (R) and Ayaan Gure pose with their infant son Muzammili, who was born in Germany, in the room they share at an asylum-seekers' shelter in Vossberg village on October 9, 2015 in Letschin, Germany. Approximately 60 asylum-seekers, mostly from Syria, Chechnya and Somalia, live at the Vossberg shelter, which is run by the Arbeiter-Samariter Bund (ASB) charity, and are waiting for authorities to process their application for asylum 2015 Getty Images Refugees settle in Germany Germany German Chancellor Angela Merkel pauses for a selfie with a refugee after she visited the AWO Refugium Askanierring shelter for refugees in Berlin Getty Images

It comes as Save that Children warned that thousands of the youngest and most vulnerable refugees were “living in fear” in deplorable conditions in amps across Europe.

Almost five months after the controversial EU Turkey deal, the number of migrants arriving over the Aegean Sea and being imprisoned on Greek islands is rising.

The number of asylum seekers attempting the treacherous crossing over the Central Mediterranean to Italy – the most dangerous voyage in the world – is also peaking.

Charity workers said around 3,800 children are among more than 10,300 refugees and migrants stranded on a handful of Greek islands, forcing them to live in unsafe conditions.

Katie Dimmer, Save the Children’s Director of Operations in Greece, said: “Families who have fled violence and death in their homeland continue to live in fear and do not feel safe.

“They have told Save the Children staff that they are too scared to let their children out of their sight due to the frequent protests and a lack of security in the camps.”