Abid Naseer, 24, and Ahmed Faraz Khan, 26, both Pakistani nationals who were arrested last year in counter-terrorism raids but never charged, were told they had won their appeal against deportation at a hearing of the Special Immigration Appeals Commission (Siac) in central London.
Mr Justice Mitting, chairman of Siac, said in a written ruling the panel was "satisfied" Naseer was an al-Qa'ida operative who "posed and still poses" a serious threat to the national security of the UK.
He said it would be "conducive to the public good" if Naseer was deported, but the tribunal was allowing his appeal because "the issue of safety on return" made it impossible to send him back to Pakistan.
The judge added that Faraz Khan - said to have undergone a "radical change of view" between leaving home and arriving in the UK - could "safely be taken to have been willing to participate" in Naseer's plans, but his appeal too was allowed on the grounds of his safety on return.
The successful appeals prompted newly appointed Home Secretary Theresa May to say that "all possible measures" are now being taken to ensure the men do not engage in terrorist activity.
She said: "Protecting the public is the Government's top priority. We are disappointed that the court has ruled that Abid Naseer and Ahmad Faraz Khan should not be deported to Pakistan, which we were seeking on national security grounds.
"As the court agreed, they are a security risk to the UK. We are now taking all possible measures to ensure they do not engage in terrorist activity."
Two other Pakistani nationals arrested with Naseer and Faraz Khan - Tariq Ur Rehman, 39, and Abdul Wahab Khan, 27, who had returned to Pakistan - lost their appeal to return to the UK.
The Siac panel said it was satisfied on the balance of probabilities that Wahab Khan was a committed "Islamist extremist" and that he and Rehman were "knowing participants" in Naseer's plans.
One other man arrested in the raids, Shoaib Khan, 31, who had returned to Pakistan, won his appeal against deportation. The judge said the panel was satisfied he was not a "knowing party" to Naseer's plans.
The judgment comes after hundreds of officers carried out raids in north-west England in April last year over an alleged bomb plot in which 12 men were arrested - including 10 Pakistani nationals on student visas and one Briton.
The raids were brought forward following a blunder by Metropolitan Police Assistant Commissioner Bob Quick. He accidentally showed secret documents with details of the plan to photographers outside Downing Street.
Mr Quick, then Britain's most senior counter-terrorism officer, later resigned saying he "deeply regretted" having jeopardised a major police operation.
All 12 suspects were released without charge with 11 of the men - all Pakistani nationals - transferred into the custody of the UK Borders Agency.
Giving his reasons for not returning Naseer and Faraz Khan to Pakistan, the judge said the panel was not prepared to accept arguments that there existed a "sufficient safeguard" against prohibited ill-treatment of the men on return.
Mr Justice Mitting said the Home Secretary's case had been that each of the men was a party to a plot to carry out a "mass casualty" attack between April 15 and April 20 last year.
The case was founded on a series of emails exchanged between a Pakistani registered email account and an email account used by Naseer, who has been described previously as the "ringleader" of the plot.
The security service's assessment was that the user of the Pakistani email account was an al-Qa'ida associate and that the messages sent from the account used by Naseer described different ingredients for explosives and identified, in general terms, the operatives who would carry out the attack.
The assessment also judged that, in an email on April 3, 2009, Naseer declared his and their intention to carry out a "mass casualty" attack between April 15 and April 20.
The ruling said it was satisfied, to the criminal standard, that the user of the Pakistani registered account was an al-Qa'ida associate.
Naseer had provided a detailed explanation of the emails, the ruling said, claiming he was searching for a wife.
The ruling rejected this explanation as "utterly implausible" and a "lie".
He had "carefully woven" an account of a real relationship with a Miss Y into a false explanation of the emails, it said, in particular the email sent on April 3.
"He did not change his mind about marrying Miss Y on the morning of April 3," it said. "We are sure that that email conveyed a sinister and alarming message to an al-Qa'ida associate."
The ruling concluded that: "We are unable to determine whether Naseer and his associates would, in fact, have been able to carry out an attack intended to cause mass casualties between April 15 and April 20. We are however satisfied, at least on balance of probabilities, that, by the April 3 email, he declared to an al-Qa'ida associate that that was his intention."
A statement issued by Sarah Kellas and Gareth Pierce, solicitors for Naseer and Faraz Khan, said: "The decision of Siac today in respect of the two students we represent is in fact, for them, the worst of all worlds.
"On the basis of secret evidence which it refuses to disclose to the students, the court tells the world in its judgment that they are closely connected to an al-Qa'ida plot to cause explosions in the UK.
"The court acknowledges they have not been told why it comes to this conclusion, yet these young men have been branded publicly and thereby exposed to personal danger for the rest of their lives.
"Siac moreover refused them permission to appeal against its decision on the basis that they had 'won'.
"At the same time Siac has decided that neither can be deported to Pakistan without the probability that he will be tortured.
"The risk of such a fate has of course been heightened but in all likelihood created by the Secretary of State's claim and Siac's decision."
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