Disclosure that applications for courts to sit in secret could themselves remain secret is described as 'deeply disturbing'

The government's plan to establish a new generation of secret courts has sparked fresh controversy after it emerged that the fact that a hearing is to be held behind closed doors may itself be kept secret.

During House of Lords debates, it was disclosed that a government application for a court to sit in secret – with the public, the media and even the claimant and their lawyers being excluded – could itself remain completely secret under the proposals.

The admission drew immediate comparisons with so-called superinjunctions, which not only prevent the media from publishing information said to be confidential or private, but also ban publication of the fact that the injunction exists.

The secrecy proposals, contained in the government's justice and security bill, allow government ministers to apply for special courtroom measures known as closed material procedure (CMP) whenever the government or its intelligence agencies are being sued in the UK courts.

Ministers say the measures are needed to prevent intelligence material handed over by friendly governments being disclosed in open court.

Many lawyers and human rights activists deny that such wide-ranging secrecy is necessary, and point out that once the bill becomes law, the public will be prevented from learning about the UK government's involvement in human rights abuses, such as the torture of Binyam Mohamed, the decision to consign British citizens to Guantánamo, and the existence of the last Labour government's secret torture policy.

Lady Stowell of Beeston, a government whip in the Lords, told peers: "As to whether the press should be notified at the point of application for a CMP, it may well be informed, but it will not be informed if the issue is related to national security."

Asked by Lord Falconer of Thoroton, the former lord chancellor, for clarification that it was the government's intention "that there will be certain circumstances when even the fact of an application … is to be kept secret", Stowell replied that not all CMP applications would necessarily be kept secret, but that "if the knowledge that the application has been made could give rise to concern about national security, it would not be made public."

The admission was described by Reprieve, the legal charity that helped represent Mohamed when he brought proceedings against the British government, as a "deeply disturbing development".

Clare Algar, its executive director, said: "This is reminiscent of superinjunctions in its excessive secrecy. Yet instead of merely covering up footballers' indiscretions, these courts could be used to sweep serious state human rights abuses, such as torture, under the carpet. If this bill passes, it will badly damage centuries of British legal tradition and make it far harder for the citizen to hold the state to account."

The Ministry of Justice said those making allegations against the government, and MI5 or MI6, would still be able to do so in public, and their claims were more likely to result in trials – albeit partly in secret – rather than being settled out of court. The media would then be able to report on the courts' decisions.

A spokesman said: "Nothing currently heard in open will go into closed session. These measures have no impact on claims that the government, or the security and intelligence agencies, have been directly involved in wrongdoing."