Damning court of appeal findings about the "dubious" involvement of security officials in the mistreatment of former Guantánamo Bay detainee Binyam Mohamed were made public today, thwarting government efforts to keep them secret.

Lawyers for Binyam Mohamed opposed the removal of the passages from the judgment on the involvement of MI5 in his torture by US agents. (Photograph: Shaun Curry/AFP/Getty Images) In a remarkable sequence of events, appeal court judges considering the case of Mohamed, who claims he was tortured, reinstated their findings about the security services, stating that some officials "appear to have a dubious record when it comes to human rights and coercive techniques".

Issuing a final judgment in Mohamed's appeal against the foreign secretary over his treatment, the judges said that the dubious record extended to "frankness about the UK's involvement with the mistreatment of Mr Mohamed by US officials".

Opposition politicians and human rights campaigners welcomed the court's decision and called for a judicial inquiry into the UK's complicity in torture. But the home secretary, Alan Johnson, remained defiant, rejecting the judges' findings.

"We totally reject any suggestion that the security services have a systemic problem in respecting human rights," he said.

"We wholly reject too that they have any interest in suppressing or withholding information from ministers or the courts."

The judgment comes after widespread criticism of government attempts to have the remarks, made by the master of the rolls, Lord Neuberger, removed from the public domain.

The government's lawyer, Jonathan Sumption QC, wrote to the court asking that the comments, contained in the draft judgment, be removed because of their "exceptionally damaging criticism" of the security services.

In what is being seen as a triumph for open justice and judicial independence, the judges largely rejected Sumption's request, placing the initial judgment in the public domain and amending the final version to clarify that the findings related to the treatment of Mohamed.

Neuberger rejected Sumption's criticism that the original version of paragraph 168 went "well beyond" the evidence heard by the high court.

The judge said its contents were "fully supported by the findings of the court based on the evidence".

The decision is likely to provoke controversy after MPs and the MI5 chief, Jonathan Evans, rejected criticism of the security services. Despite coming under pressure to water down its findings, the court repeated its powerful criticism today.

"[The record of security service officials] regrettably, but inevitably, must raise the question of whether any statement in the certificates on an issue concerning such treatment can be relied on … Not only is there an obvious reason for distrusting any UK government assurance based on SyS [security service] advice and information, because of previous 'form', but the Foreign Office and the SyS have an interest in the suppression of such information."

In the statement the judges took the unprecedented step of waiving confidentiality and reading out previously unpublished remarks about the conduct of MI5.

Significantly, the verdict clarified the judges' views of the responsibility of the foreign secretary in Mohamed's case.

The statement said: "The good faith of the foreign secretary is not in question, but he prepared the certificates partly, possibly largely, on the basis of information and advice provided by SyS personnel."

Nevertheless, the Liberal Democrat foreign affairs spokesman, Edward Davey, said the judgment was "deeply embarrassing" for the foreign secretary, David Miliband, as it implied he "had the wool pulled over his eyes".

Former home secretary David Davis, who raised the Mohamed case in parliament, accused the government of "bullying" the court and said a judicial inquiry was necessary "both to re-establish Britain's moral reputation, and allow agencies to put this behind them in continuing their battle against terrorism".

Shami Chakrabarti, director of the civil rights group Liberty, described the case as "devastating" for the security services.

"You cannot have morale in your security services or public confidence if you're not being straight about the mistakes of the past," she said.