The prime minister has ordered a new investigation into how MI5 gave false evidence to three courts about conversations with the BBC.

Sir Keir Starmer’s direction follows requests from the High Court and Investigatory Powers Tribunal, which both rejected MI5’s explanations about what happened.

The case centres on a neo-Nazi state informant known as Agent X who used his MI5 role to coerce his girlfriend, whom he attacked with a machete.

On Tuesday, the prime minister wrote to the Investigatory Powers Commissioner Sir Brian Leveson directing him to conduct a new inquiry.

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

He said the 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 the relevant courts had found that MI5’s investigations into the false evidence “suffered from serious procedural deficiencies”.

In February, the BBC revealed that MI5 had lied to three courts while defending its handling of the misogynistic MI5 agent, whom the BBC had sought to expose in a 2022 investigation.

Arguing for secrecy, the Security Service told judges it had stuck to its policy of not confirming or denying informants’ identities.

In fact, MI5 had disclosed the Agent X’s status in phone calls to me, as it tried to persuade me not to investigate him. The service aggressively maintained its position until I produced evidence proving it was untrue, including a recording of one of the calls.

Following the BBC’s revelations, MI5’s Director General Sir Ken McCallum apologised. Two official inquiries then took place which absolved MI5 and its officers of deliberate wrongdoing, claiming the false evidence was down to mistakes and poor memories.

But, in July, a panel of senior high court judges ruled that the “investigations carried out by MI5 to date suffer from serious procedural deficiencies” and that “we cannot rely on their conclusions”.

They said it would be “premature” to decide whether to begin contempt of court proceedings against any MI5 officers before a new investigation took place.

Later the same month, the investigatory powers tribunal also rejected MI5’s explanations and requested a new investigation.

The new investigation will be carried out under the auspices of the Investigatory Powers Commissioner Sir Brian Leveson, who has oversight of MI5’s surveillance activities. His office, IPCO, was also provided with false evidence by MI5 in the case.

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.

“Both courts concluded that further investigation was necessary to determine how incorrect evidence came to be presented to them. The government accepted their recommendations and the Prime Minister has commissioned Sir Brian Leveson – the Investigatory Powers Commissioner – to lead this investigation. It would be inappropriate to comment further until it is completed.”