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.
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.
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.”
There have been numerous reports of rape and abuse on the journey to Europe, including by people smugglers, as well as a string of assaults in refugee shelters and in “The Jungle” camp in Calais.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in