Sir Keir Starmer’s instruction follows requests from the High Court and the Investigatory Powers Tribunal (IPT), both of which rejected MI5’s explanations. The case concerns a neo-Nazi informant known as Agent X, who exploited his position to coerce his girlfriend, later attacking her with a machete.

On Tuesday Sir Keir wrote to the Investigatory Powers Commissioner, Sir Brian Leveson, directing him to launch a new inquiry.

In a written statement, he said: “I have now issued a direction to the Commissioner to commence this investigation immediately.”

He added that courts “will use the outcome of this investigation to determine their next steps in relation to the case of Agent X.”

Sir Keir noted that judges had found MI5’s earlier investigations into the false evidence “suffered from serious procedural deficiencies”. In a letter to Sir Brian, he said the courts had “rightly expressed their displeasure at MI5 for providing this false evidence”.

The inquiry will be led by the Deputy Investigatory Powers Commissioner, Sir John Goldring, supported by a small team. Sir John previously oversaw the Hillsborough inquests.

The BBC reported in February that MI5 had misled three courts while defending its handling of Agent X, who it tried to prevent from being exposed in a 2022 investigation. Judges were told the service had stuck to its policy of not confirming or denying informants’ identities. In fact, MI5 had disclosed Agent X’s status in phone calls to a BBC journalist, who later produced recordings of the conversations.

Following the revelations, MI5 director general Sir Ken McCallum apologised. Two official inquiries cleared the service and its officers of deliberate wrongdoing, blaming mistakes and poor memory.

But in July, senior High Court judges ruled MI5’s investigations “suffer from serious procedural deficiencies” and that “we cannot rely on their conclusions”. They said it was “premature” to decide on contempt of court proceedings against officers until a new investigation was completed. The IPT later also rejected MI5’s explanations, raising wider concerns about whether the duty of candour had been upheld and whether government lawyers might have been involved.

Sir Brian Leveson confirmed his team would have access to legally privileged material if required. The inquiry’s remit is to examine how false evidence was given to the courts, the extent of compliance with the duty of candour, and who was responsible.

A Home Office spokesperson said: “The Home Secretary is concerned that inaccurate evidence was provided to the High Court and Investigatory Powers Tribunal. The Director General of MI5 has rightly apologised for this serious failing, both publicly and to the courts.”