She said: "We are now taking all possible measures to ensure they do not engage in terrorist activity."
Altogether five men - who had been tracked by MI5 before the raids last year - also appealed against deportation.
Abdul Wahab Khan, 27, and Tariq Ur Rehman, 38, who were also arrested at the time, lost their appeals. They had already returned to Pakistan.
Mr Justice Mitting said they were committed Islamists who knew of Mr Naseer's plan.
Mr Ur Rehman denied this and told the BBC: "I have no link with al-Qaeda; I am not an Islamic extremist. I am a normal Muslim - I go to the mosque and pray."
A fifth man, student Shoaib Khan, won his appeal, with the court saying there was no evidence of wrongdoing against him.
His lawyer Amjad Malik told the BBC that his 31-year-old client, who is also currently in Pakistan, wanted to return to the UK to resume his studies.
Much of the detail in the case was presented to Siac - a court which deals with such cases - in secret during the past three weeks.
The independent reviewer of terrorism legislation, the Liberal Democrat peer Lord Carlile, said he hoped the government would look more creatively at the issue.
"We do not want people who have been held to be terrorists walking our streets," he said.
WHERE ARE THEY NOW
Abid Naseer: In prison under immigration powers
Faraz Khan: Bailed to a secret location, movements restricted
Tariq ur Rehman: Voluntarily returned to Pakistan
Abdul Wahab Khan: Voluntarily returned to Pakistan
Shoaib Khan (cleared): Voluntarily returned to Pakistan but wants to resume studies in UK
"We therefore have to start looking for a different way of dealing with individual cases.
"I hope very much that this new government will start looking more imaginatively than the previous government at ways of returning people to their home country with a form of verification that they're treated properly in that country."
BBC home affairs editor Mark Easton also said it was likely that a control order would be used to restrict the movement and activities of the two men and to keep them under constant watch, although ministers would be unable to confirm this.
However, he said this was also an issue of contention between the two parties.
The Lib Dems have described the orders as "an affront to British justice" while the Conservatives have said a review is needed.
Shami Chakrabarti, director of human rights group Liberty, said: "It's no surprise that on the day that this issue about deporting a terror suspect comes up that people start wobbling over the Human Rights Act.
"But here's the thing - sending people to torture is not just unlawful, it's wrong.
"We sometimes call it extraordinary rendition - and both the Conservatives and the Liberal Democrats have said how wrong that is and have promised in Opposition to set up an inquiry."
CCTV shows police breaking down the door of a property in Manchester
In all, 11 men were detained after police raided a series of locations across Liverpool, Manchester and Lancashire in April 2009.
Ten of them were from Pakistan, who were all either close friends or loosely known to each other.
At the time officials feared an imminent attack.
But no explosives were found and all of the men were released without charge after two weeks.
They were immediately detained again under immigration laws after the then home secretary sought their deportation, saying they were still a threat to national security.
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