A primary school-aged child has had details of their referral to the government’s controversial anti-radicalisation Prevent programme deleted by the Metropolitan police following court action, the Guardian can reveal.

Following a settlement that remains confidential, the child will see all relevant records deleted, including from the Prevent case management (PCM) database, the existence of which was revealed by the Guardian and Liberty in October. The referring authorities also agreed to correct and delete relevant records.

As details of the case are disclosed, the Guardian can reveal that Counter Terrorism Policing Headquarters (CTPHQ), the Home Office and several police forces across England and Wales have refused to reveal how many individuals are on the database following requests made under the Freedom of Information Act.

Lawyers at Deighton Pierce Glynn (DPG), acting for the parents and the child, said their client feared the records could be used against them in the future, even though they were based on a mistake. The legal team relied on the Data Protection Act and Human Rights Act to secure deletion of the relevant Prevent records.

Without deletion, DPG said, the records would have been retained for at least six years under the police’s national retention assessment criteria (NRAC) policy, which does not differentiate between records of adults and children.

The Met refused to give any reassurance that the records would not be used again in relation to the child and would not feature in any Disclosure and Barring Service criminal record checks against them as an adult, DPG said.

Daniel Carey, partner at DPG, said: “The police’s data retention policy – the national retention assessment criteria – fails to recognise the non-criminal nature of Prevent referrals and doesn’t distinguish records relating to very young children, creating real concerns and worries for parents that these records will continue to affect them in later life.

“My client’s parents were concerned that it took a lot of legal action simply to erase Prevent records based on a clearly mistaken referral. There are obvious implications for the many other Prevent referrals made regarding schoolchildren and the effect that such enduring records may have on them in the future.”

DPG threatened the Met police with a judicial review and the force agreed to settle and delete the details before the case came to court. The Met declined to comment.

The stated aim of Prevent, a voluntary programme, is to divert people away from terrorism before they offend and crucially deals with individuals who have yet to cross the criminality threshold.

Fresh figures on Prevent referrals released on Thursday revealed that there were 5,738 referrals in the year to March 2019, only 10% of which – 561 cases – led to the supply of specialist support. The rest left the process or were referred to other services, such as the education sector.

The PCM database is managed centrally at CTPHQ. Prevent practitioners in police forces across the UK are able to enter referrals to Prevent into the database. External agencies, including the Home Office, which is responsible for MI5, are able to request information from the database. Individuals are not told that their details are being held.

In October, when the Guardian revealed the existence of the database, CTPHQ said it allowed them to be “accountable”.

The Guardian sent freedom of information requests to CTPHQ asking for the total number of individuals on the database, as well as the numbers of Prevent practitioners able to access it. The request was refused.

Similar requests were sent to all police forces in England and Wales, asking to provide how many entries had been made. At least 23 of them have rejected the request, most citing the risk of identifying individuals as one of the key reasons.

However, one force, Merseyside police, did provide the information. It created 660 individual PCM records but added that “several persons and institutions” had multiple records as they had been referred numerous times, so the figure did not equate to individuals.

The Home Office refused when asked to reveal how many times it had requested information from the PCM database.

The CTPHQ’s national Prevent coordinator, Ch Supt Nik Adams, said: “The public would expect us to keep records of people vulnerable to radicalisation, so that we can understand when risks increase, provide support and take action against the causes. This is especially relevant in the case of children, and our priority is to protect them as potential victims of extremists.

“We take our responsibilities to protect people’s personal information seriously and records are regularly updated and deleted when it is no longer necessary or proportionate to keep them.”

Rosalind Comyn, Liberty policy and campaigns officer, said: “It’s sheer hypocrisy for police chiefs to claim the Prevent database provides transparency and then refuse to answer basic questions about it. Thousands of people, including children, could be on this database because of what they’re perceived to think or believe. As a bare minimum, the government and police must tell people they are on the database, what information is held on them and how it can be used.

“This database isn’t about keeping us safe – it’s about keeping tabs on people. Those in power must stop shrouding Prevent in secrecy and shielding it from the robust independent review it so desperately needs.”