Legal principle established in 1637 banned secret talks between lawyers and courts. It was broken by the government

When the master of the rolls, Lord Neuberger, decided to retract paragraph 168 from his draft judgment in the case of Binyam Mohamed, he relied on almost 400 years of jurisprudence to assume that the parties in the case had agreed to its removal.

The case of Ship Money, brought by Oliver Cromwell's cousin John Hampden in 1637, established the principle that there should be no secret communication between lawyers and the courts in legal proceedings.

Representations from one side – in this case, the foreign secretary's barrister, Jonathan Sumption QC – should be copied to all other parties in the case, so that they have the opportunity to respond.

On that basis, when Neuberger received a letter from Sumption requesting removal of the paragraph from the court of appeal draft judgment, lawyers say he must have thought he was acting with the agreement of all parties.

Neuberger removed the paragraph from the final judgment, watering down the court's condemnation of the security services, described by Sumption as containing "exceptionally damaging criticism".

"The master of the rolls' observations … will be read as statements by the court that the security service does not in fact operate a culture that respects human rights or abjures participation in coercive interrogation techniques," says Sumption's letter, now published in full on the Guardian's website.

But other parties in the case were not consulted and are furious.

"In all the years – I was first a government lawyer and then a liberty lawyer – I have never known the draft judgment process abused in this way," said Shami Chakrabarti, director of Liberty, the human rights organisation which was a party to the case. "The purpose of using drafts is for typographical and factual corrections – minor matters such as names and dates.

"It is not to allow one party to re-run substantive arguments and tempt a court to tone down or change its judgments."

She added: "I can't believe that the Foreign Office thought they could get away with this. It shows the kind of contempt for the law that this case has always been about."

"This is anti-constitutional behaviour of the most disquieting kind," said Mark Stephens, who represented a group of American newspapers in the case and was not informed of Sumption's letter to the court until yesterday, when the judgment had already been changed. "In my experience of 31 years practising as a lawyer, it is unprecedented.

"This conduct has embarrassed Lord Neuberger who clearly assumed that he had received all submissions when he reached his decision to remove the judgment."

In a remarkable series of events, Neuberger has admitted he may have been "over-hasty" to remove the findings, after the Guardian, as well as Liberty and Justice, challenged the exclusion.

"I think it was over-hasty to amend that written request of one party, without giving other parties the opportunity to reply," said Neuberger.

Answering questions in the Commons today, the foreign secretary, David Miliband, defended the attempt to have the paragraph removed from the judgment.

"What our counsel did, once he had been provided with copy of the judgment in draft, was to express real concern that one paragraph set out conclusions that went beyond the evidence concluded and risked causing prejudice to a criminal investigation," said Miliband. "Our counsel took the view that this should be brought to the attention of judges in case."

Miliband came under fire from MPs for the conduct of the Foreign Office, for attempting to have the paragraph retracted, and for the court's findings that seven paragraphs kept secret from an earlier Binyam Mohamed judgment should also be kept secret.

The paragraphs, which have now been released, were redacted after Milliband said their publication would damage the government's intelligence-sharing relationship with the US administration.

"Publication of the redacted paragraphs would not reveal information which would be of interest to a terrorist or criminal or provide any potential material of value to a terrorist or a criminal," said Lord Chief Justice Lord Judge in today's judgment. "It increasingly appears that the issue is the control principle rather than the confidentiality of any information within the redacted paragraphs themselves."

"This whole case was one about openness, and attempts by the government to cover-up torture instead of exposing it," said Chakrabarti. "The fact that even at the court door, before the ink has even dried on the court of appeal's judgment, the government has had yet another go at a cover-up is truly remarkable."