He said it meant the accused could not be extradited to the US on copyright grounds.
Instead, Justice Gilbert said there were "general criminal law fraud provisions" which covered the actions of the accused and they could be extradited on that basis.
He said he agreed with district court Judge Nevin Dawson that there was enough information to make the decision based on accepting a "record of the case" put forward by the US which detailed the evidence it claimed to hold against the Megaupload accused.
Dotcom's lawyer, Ron Mansfield, claimed victory from the ruling, saying the case was no longer the "largest criminal copyright case".
"As we have said all along, there is no such offence under our Copyright Act. We were right."
Mansfield said: "To win the major plank of the case but to get that outcome is extremely disappointing. It is hard to accept the logic that, if the conduct that all accept at its heart relates to assertions of breach of copyright ... how it can nonetheless be massaged into a general fraud offence."
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