A promise to end routine strip-searching of children in custody is being flouted, according to data revealing there were more than 43,000 recorded incidents involving children as young as 12 over a 21-month period – but in only 275 searches were illicit items found.

Contraband was discovered in eight of every 1,000 searches in young offender institutions and secure children's homes and training centres in the course of one year, and just three in the next year. Tobacco was the most common item found, with no recorded discoveries of drugs or knives.

A leading children's rights campaigner described the practice as "institutionalised child abuse" after a freedom of information request identified that a total of 43,960 such searches, which routinely involve the children being made to strip naked, were carried out in 21 months.

Two years ago, the Youth Justice Board announced that the routine strip-searching of incarcerated children would stop. Its press release said children had described the practice as undignified, leading "to feelings of anger, humiliation and anxiety".

But the information obtained under FOI and seen by the Guardian shows children were made to strip naked 43,960 times in 25 young offender institutions (YOIs), secure children's homes (SCHs) and secure training centres (STCS) in the 21 months up to December 2012.

The youngest person to be strip-searched was 12. Nearly half – 48% – of children strip-searched were from black and minority ethnic communities. Physical force was used on children being searched 50 times.

The FOI request was made by Carolyne Willow, former national co-ordinator of the Children' Rights Alliance England. She described the "practice of children being forced to expose their naked bodies to adults in authority as institutionalised child abuse".

At the end of August 2012, there were 1,643 children in custody in England and Wales, of whom 1,225 were held in YOIs, 269 in STCs and 149 in SCHs. Of those, 64 were aged under 14 and two just 12. The cost of keeping children in the secure estate was £268.9m.

In 2006, Lord Carlile QC conducted an inquiry into the use of restraint, strip-searching and segregation in child custody. Then, as now, fewer than 10% of searches yielded a "find" and tobacco was the most common item discovered.

One 16-year-old girl told the inquiry she had been strip-searched and ordered to hand her sanitary towel to staff.

Another girl recalled: "When I had my first full search it was horrible as I have been sexually abused and I didn't feel comfortable showing my body as this brought back bad memories."

Willow said: "This matter is of such magnitude that ministers must amend the rules governing secure establishments to prescribe the extremely limited circumstances in which it would ever be permissible to make children in institutions remove their clothes and underwear."

John Drew, chief executive of the YJB said full strip-searches should only be used following an assessment of risk and this should be the starting point for practice in all secure establishments.

He added: "Where providers of STCs and YOIs consider it necessary to carry out routine full searches on first admission, this approach should be justified and will be kept under review by the YJB."

A spokeswoman for the Ministry of Justice said a revised searching policy for young people was introduced last March that ensures their safety and security while not subjecting them to a full search unnecessarily.

"Full searches will only take place when it is necessary and there is a clear justification or identified risk. We have a duty to keep any item that could endanger the safety of young people out of secure establishments. We use a number of measures to disrupt their supply and searches are an important part of this."

The routine strip-searching of women prisoners ended in 2009, after a review undertaken by Lady Corston.

• This article was amended on 5 March 2013. The original referred to incidences, rather than incidents, involving children, and has been corrected.