Children in custody are still not safe from sexual abuse after more than 1,000 attacks were alleged from 2009 to 2017, a statutory inquiry has found.

Prof Alexis Jay, the chairwoman of the independent inquiry into child sexual abuse, said on Thursday she was deeply disturbed by what the inquiry found as it published a report that described the scale of alleged abuse in young offender institutions (YOIs) and secure training centres (STCs) as “shockingly high”.

During the inquiry it was alleged that a female member of staff masturbated children at Medway STC in 2015; and that in 2014, members of staff at Rainsbrook STC allowed two young people to go into a room together, knowing that one was going to defecate on the other’s face.

The inquiry said the report included many other recent examples, often involving allegations of staff inappropriately touching detainees during body searches or instances of restraint. It added that many more complaints of child sexual abuse in custody had been made than revealed in official figures, including those published by HMs Inspectorate of Prisons.

It said there were 1,070 incidents of alleged sexual abuse in YOIs and STCs reported from 2009 to 2017.

“This number is shockingly high, given that there has been a significant drop in numbers of detained children over that time,” the report said. “The current population is around 900.”

Only nine alleged incidents resulted in criminal charges, of which four resulted in convictions.

The inquiry found that the institutions had been “very poorly resourced” and that staff turnover was running at unacceptably high levels in YOIs and in STCs, “with low morale and inadequate training, including safeguarding training”.

“There has been a shocking decline in safety in the secure estate in recent years,” it said. “This has been caused by management instability and staffing losses. There is some evidence that these have been linked to budget cuts … There is little doubt that YOIs and STCs were in crisis by the end of the inquiry’s investigation period.”

Evidence from adults who were sexually abused while in custodial institutions as children has been also included in the report.

“The harrowing accounts of non-recent child sexual abuse within custodial institutions were some of the worst cases this inquiry has heard,” said Jay.

One witness said that when he was 11 he was sexually assaulted by two members of staff at the same time and another witness said he was raped and sexually assaulted 35 times by four members of staff and a former pupil at Stanhope Castle, an approved school. On several occasions he was choked unconscious.

“But I am also deeply disturbed by the continuing problem of child sexual abuse in these institutions over the last decade,” Jay said. “It is clear these children, who are some of the most vulnerable in society, are still at risk of sexual abuse. I hope our report and recommendations can help protect them better in future.”

The number of children in custody has declined since mid-2008, from more than 3,000 to about 900 at any one time.

The report looked at the alleged sexual abuse and exploitation of children held in secure units since 2009, including at Feltham and Werrington YOIs, Medway and Rainsbrook STCs and Vinney Green and Aycliffe secure children’s homes.

The inquiry is now calling on the Department for Education and the Youth Custody Service to launch a full review of whether placing children in secure homes increases the risk of sexual abuse. It also wants the Ministry of Justice to ban the use of “pain compliance techniques”, which includes methods such as bending of a child’s thumbs and wrists. It said this amounted to child abuse but its use had been recorded 119 recorded times from March 2016 to March 2017 alone.

The justice minister Edward Argar said details in the report were “shocking” and pledged to urgently consider the findings. “We have recognised the need for fundamental reform of youth custody to ensure that the safety, welfare and rehabilitation of young people are prioritised across all aspects of the system,” he said.

“As part of this we are already conducting an urgent review into safeguarding in the youth estate, are rolling out new specialist training for staff and have commissioned an independent review of pain inducing restraint techniques. In addition, we increased frontline Youth Custody Service staff by over a third in 2018 and are completely changing our approach by investing in Secure Schools that will put education at heart of youth custody.

Ministers have commissioned Charlie Taylor, chairman of the youth justice board for England and Wales, to undertake an independent review of pain-inducing restraint techniques to conclude this summer.

Concerns about abuse in the institutions has been growing for several years. In February 2016, the Guardian revealed that serious allegations of abuse and bullying by staff at Medway had been reported by a whistleblower, Nathan Ward, more than a decade before.

G4S, which ran Medway, was stripped of the contract. In 2014, G4S, Serco and the Youth Justice Board paid out a combined figure of almost £100,000 in damages to 14 children who had been abused at STCs between 2004 and 2008 and other similar civil actions are pending.

In January this year, a report into the alleged abuse of children at Medway found that a series of failings led to “erratic and ineffective” monitoring of investigations into the claims.

A serious case review criticised a contract between the Youth Justice Board and Barnado’s, saying the contract “expressly did not allow” the charity, which was acting as an independent advocate for children at Medway, to refer concerns about child protection to the local authority responsible for their welfare.