An allegation that a Rwandan police commander sexually assaulted a child refugee has rocked an EU-funded scheme, under which hundreds of refugees and asylum seekers have been evacuated from detention centres in Libya.

The allegation was made by a 16-year-old Eritrean boy, who had returned to Gashora transit centre, south of Kigali, after a coronavirus-related curfew on 13 April.

Refugees say the boy was detained there along with three others – an Eritrean and two Sudanese boys – between 6.30pm and 10.30pm, and picked out by the police commander in charge.

“(He) ordered him to take off his clothes,” said a refugee leader who spoke to the teenager afterwards. “The kid did as he was told since he thought he was going to be searched, but then he was asked to take off his pants, which he refused. The commander slapped and beat him all over his body using a stick. Then he proceeded to take out his gun and threaten him with it, but [the teenager] managed to escape.”

UN refugee agency spokesperson Elise Villechalane said her office is “deeply concerned” about the “alleged case of sexual abuse against a refugee at the Gashora emergency transit mechanism. Our protection teams are present at the centre and appropriate measures have been taken to provide the alleged victim with all the necessary support, including legal and psychosocial assistance.”

Rwanda’s police force has accused the refugees of lying, saying they were unhappy with coronavirus-related restrictions and that the boy was drunk.

“They conspired to make up a story of physical and attempted sexual assault. Preliminary findings show that the complainant used the occasion to try to avoid punishment for violating curfew and instead raised other grievances about the food menu, medical services, and police presence at the camp,” the organisation said on Twitter.

The police said refugees had been playing music in the week commemorating the 26th anniversary of the Rwandan genocide. Refugees said they were listening to a preacher read prayers in the run-up to Eritrean Easter. “When everyone wants to pray they use the speaker and everyone prays in [their] room, because everyone was using social distancing,” said one man.

“Still the commander is there, circulating all the time,” another said.

The Rwandan government did not respond to requests for comment, but confirmed an investigation is underway.

Most of the refugees evacuated to Rwanda are survivors of sexual or physical abuse and spent months or years in Libya with smugglers known to torture victims who can’t pay large sums of money. They were then caught trying to cross the Mediterranean to Europe and were locked up in detention centres associated with the UN-backed Libyan government, where forced labour, food deprivation and other abuses have been reported.

Evacuees arriving in Rwanda have been interviewed for the chance to be resettled. The first groups left for Sweden and Canada earlier this year, before the pandemic forced resettlement to be put on hold.

Libya’s refugees face being cut off from aid due to coronavirus Read more

On Thursday refugees in Gashora held a protest presenting seven demands, including a proper investigation, the removal of the commander from the centre, and for a UNHCR staff member to be present at all times for their safety.

They also asked for Alight (formerly the American Refugee Committee), responsible for the protection of minors, to be replaced. Refugees said the organisation is not active or responsive. Alight did not reply to the Guardian’s request for comment.

The Guardian has visited Gashora twice, most recently last month, shortly before the lockdown. Refugees have repeatedly said they are happy to follow restrictions. Many have had tuberculosis or other health problems, making them vulnerable.

On Saturday, refugees told the Guardian they were growing increasingly upset and frustrated that the alleged assault was not being taken seriously. “[There is] no fucking justice in this society,” said one Eritrean in his 20s. “They want to suppress our voice totally. They will fade this incident and we can’t do anything about it because we are refugees.”