"You're kidding," Justice Anthony Payne said on Thursday after learning the Commonwealth had decided to withdraw funding for Adam Cranston.
The son of former deputy tax commissioner Michael Cranston was found guilty alongside four others including his younger sister of conspiring to commit tax fraud and money laundering in March.
His father was found not guilty by a court in 2019.
The Plutus Payroll scheme, described by Cranston as the "Ben Hur" of tax fraud in a recorded conversation, diverted at least $105 million from government coffers.
The guilty verdicts came after a mammoth nine-month trial and a jury deliberating for several weeks.
Lauren Cranston was sentenced to at least five years' jail on Monday.
Her four co-conspirators are awaiting their sentences, but a judge has criticised a decision to withdraw government funding for her brother's legal representation, which would be "fundamentally unfair".
Justice Payne previously "reluctantly" agreed to vacate a trial in January 2021 after learning Cranston would not be in a position to defend himself, even with the judge's assistance.
"I urge Legal Aid NSW and the Commonwealth Attorney-General's Department to reconsider their respective decisions to decline to provide Mr Cranston with legal aid to fund representation at the trial," the judge said at the time.
The Commonwealth stepped in, but has withdrawn as of Monday.
The judge was "profoundly unhappy" to find out about it on Thursday morning.
"The new attorney-general has decided the Commonwealth, having funded this for two years, is going to drop out now?" Justice Payne asked.
"(Attorney-General Mark) Dreyfus has personally decided this has he?"
A solicitor appearing for the government said that was their understanding.
"I am lost for words," the judge said.
Later finding some, he ordered transcripts be sent to Mr Dreyfus' office and NSW LegalAid.
"This tug of war between the Commonwealth and states in certain areas is profoundly unhelpful," he said.
"I think there is a significant public interest in setting out what's happened and the operation of our criminal justice system in a very serious case."
He ordered documents be tendered when Cranston's matter returns to the NSW Supreme Court on Tuesday, indicating he will write a judgment if the attorney-general's position remains the same.
"I'm not going to say anymore," he said.
Mr Dreyfus' office has been contacted for comment.
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