They have now been made public in what Igor Judge, the lord chief justice of England and Wales, said was in "the interests of open justice".
Neuberger's suppressed comments came in a ruling ordering the release of information about the case of Ethiopian-born Mohamed, who was detained for nearly seven years, including more than four at Guantanamo.
Mohamed claims he was "tortured in medieval ways" and alleges British security service MI5 colluded with US agents in his interrogation in Pakistan in 2002.
Earlier this month, he won a legal bid to force disclosure of evidence about his case despite objections from Foreign Secretary David Miliband, backed by the US government.
Britain had argued that publishing the information could endanger its intelligence-sharing relationship with the United States.
After Friday's latest twist in the case, Miliband dismissed suggestions that MI5 had lied over its involvement in Mohamed's case and said he was disappointed at the decision to publish Lord Neuberger's comments.
Prime Minister Gordon Brown insisted he had "every confidence" in the security services, but said he would publish revised guidelines on the treatment of detainees held overseas "shortly".
"We condemn torture without reservation," Brown said. "We do not torture, and we do not ask others to do so on our behalf. We are clear that officials must not be complicit in mistreatment of detainees."
Reprieve, the campaign group representing Mohamed, called for an inquiry into the claims, echoing a demand made by Britain's human rights watchdog.
Police are already investigating allegations that the intelligence services were complicit in the abuse of Shaker Aamer, Britain's last inmate still at Guantanamo.
Neuberger said the British security services had denied knowledge of any ill-treatment of US detainees.
"Yet, in this case, that does not seem to have been true: as the evidence showed, some security services officials appear to have a dubious record relating to actual involvement -- and frankness about any such involvement -- with the mistreatment of Mr Mohamed when he was held at the behest of US officials," said the judge.
Neuberger added there were questions over whether statements about alleged mistreatment could be relied upon because "the security services have an interest in the suppression of such information".
Judge, the lord chief justice, said although ministers had not interfered to prevent Neuberger's comments being published, the "most effective way of dispelling any lingering public perception" that this had happened was to allow them to be made public.
Miliband said he "completely" rejected "any suggestion of lies" and added that while judges had a right to express their opinions "the government doesn't have to agree with everything they say".
"Ministers take incredibly seriously the dual commitments that we have to uphold our laws and our ethics on the one hand and to protect national security on the other," he said.
Home Secretary Alan Johnson said he was "deeply disappointed" by the criticism of the security services.
"We totally reject any suggestion that the security services have a systemic problem in respecting human rights," he said.