This came despite the fact that Siac acknowledged one was a threat to national security and the other was a member of a banned group.
Home secretary John Reid made clear his objections to the ruling but admitted at the time that the final decision was not his jurisdiction.
Earlier today the BBC reported Mr Reid agreed in principle with the release of the suspects, but a Home Office spokesperson denied this was the case.
"The home secretary is strongly opposed to bail," the spokesperson said.
He added: "We believe these individuals should be detained, particularly since Siac has agreed that at least two of these individuals are a threat to the national security of the UK".
Last week's test case ruling flew in the face of Home Office policy, which supports the deportation of terror suspects to all countries where there is no risk of torture.
Libya's leader, Colonel Gadaffi, has said in a bilateral agreement with Britain that his country will not engage in torture but critics argue the pledge would be unlikely to be honoured.
The Home Office has requested that the two men's bail have strict conditions imposed.
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