By Martin Evans, Crime Correspondent

The man, who is believed to work for MI5, is charged with two counts of common assault, one count of sexual assault and one count of harassment.

His case will take place at Southwark Crown Court, but in a highly unusual move, his identity will be protected throughout.

He has been given the pseudonym, Mark Barton, and will give evidence from behind a screen so that even the jury will not see his face during the trial.

The media will be prevented from describing his physical appearance and anyone breaching the order could find themselves in contempt of court.

At a pretrial hearing yesterday Judge Alistair McCreath agreed to grant the spy anonymity on the grounds that there could be a “real and immediate risk to his life”.

The application to ask the court for anonymity was made by the prosecution, rather than the defence, with lawyers for the Crown Prosecution Service arguing that Mr Barton should be protected under Article Two of the European Human Rights Act, right to life.

The case has raised a number of concerns over the increasing threat to democracy presented by so-called secret justice.

Lawyers acting on behalf of the media challenged the application arguing that such a decision would be against the principles of open justice.

But Judge McCreath said he was satisfied it was in the public interest to keep the identity of the accused secret.

He said: “The defendant in this case, charged under a pseudonym Mark Barton, works for the security services.

“The allegations against him, of course unproven, relate to alleged misconduct by way of harassment and sexual assault and otherwise in relation to an unidentified woman who is also a member of the security services.

“I recognise that before I can grant anonymity to this defendant and along with it the physical concealment of him while he sits in court and gives evidence I must be satisfied that there is a real and immediate risk to his life I anonymity is not granted.

“The material before me, which I cannot obviously specify, satisfies me that the risk is real, in the sense that it is objectively verified, and I’m satisfied that it is immediate, in the sense that it is present in the circumstances if anonymity is not granted.”

The judge said by protecting the identity of the spy, it would ensure that the evidence would be heard in open court and could be fully and freely reported.

He explained that the alternatives to granting the prosecution application would be to have no trial at all or hold the hearing in secret, a move he described as “wholly unwarranted”.

In conclusion he said: “I direct that the trial of this defendant take place under a pseudonym and that during the course of the trial his physical identity will be concealed by whatever practical means are the most appropriate.”

The accused has not yet entered any pleas to the charges and date for the trial is yet to be fixed.