Children at a scandal-hit jail set to close in three months are still being subjected to pain-inflicting techniques during physical restraints, despite repeated warnings against using what inspectors have called “unacceptable” practice.

Medway secure training centre for 12- to 18-year-olds has been dogged by allegations of mistreatment of the young inmates by staff for years.

The latest inspection by Ofsted, conducted in October, found the experience of children at the centre near Rochester, Kent, was inadequate due to serious concerns over the way staff managed serious and significant incidents.

Use of force had increased significantly and pain-inflicting techniques continued to be used on children, the inspection found. Ofsted called for staff to “immediately cease using pain-inducing techniques on children during physical restraints”.

In a centre that at the time of inspection was holding 29 children, there were 359 incidents involving force recorded in the previous six months, with 115 incidents in September alone. Three-quarters of incidents in September, about 85, related to two children alone.

The increase in the use of force led to a deterioration in governance and oversight of the practice, inspectors found, with a backlog of 150 use of force incidents dating back three months that had not been quality assured.

Campbell Robb, the chief executive of Nacro, which provides education programmes in Medway praised in the report, said he was proud of the work the staff did, adding: “But the truth is we are operating in a broken system. Despite the best efforts of staff working in the regime, there are serious failures across the system from significant increases in the use of force to a failure to safeguard children at risk from harm. This is simply unacceptable.

“So many of the children in the system have for too long been overlooked and written off. Often impacted by violence, trauma and abuse earlier in their lives, children arrive at settings such as Medway in need of care, support and guidance.

“But we are only one part of the system and things have to change. The new government must commit to fundamental reform to give all children caught in the youth justice system the best chance at a second chance. Our justice system has for too long been under-resourced and overlooked. It is time for change.”

Medway STC is publicly-run but was previously operated by the private company G4S, which was stripped of its contract in 2016 shortly after an undercover Panorama documentary alleged that staff at the centre were abusing inmates. A Guardian exposé also revealed a history of abuse allegations at the centre.

Frances Crook, chief executive of the Howard League for Penal Reform, said: “We all want children in trouble with the law to grow up to be law-abiding citizens. This damning report tells us Medway is risking the exact opposite.

“The Howard League took legal action in an attempt to stop Medway being built. We argued that it would become a place of abuse, and it has. Thousands of children have suffered the consequences.

“It is time that it was closed and we start investing in approaches that will actually work to help children grow out of crime.”

After the centre closes in March, the site is to be turned into the country’s first secure school – an education-focused alternative to youth jails – that will be run by an academy trust that specialises in schools in deprived areas.

A Ministry of Justice spokesperson said: “Medway holds some of the most challenging young people in the country and our staff work tirelessly to keep them safe – but, given safety is our priority, this is a disappointing report and we need to do more.

“We have acted quickly to introduce a new rapid review process for every use of restraint and the independent review we commissioned into the use of pain-inducing techniques will be published in the new year, alongside the actions we will take as a result.

“Medway will close in the spring so the site can be transformed into the first ever secure school, representing a major step towards our commitment to putting education at the heart of youth custody.”