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Graeme Mark Lowery (54) had denied charges of wilfully ill-treating an animal and preventing the course of justice and spent this week in the dock at the Dunedin District Court.
However, yesterday Judge Michael Crosbie sent the jury home and declared a mistrial.
The specific reasons for the ruling and what he told jurors before dismissing them cannot be published, to ensure fair-trial rights are preserved.
The trial had been delayed earlier this week when it emerged there was evidence that had not been previously provided to the prosecution or the defence.
Judge Crosbie said the material was not new - "it had always been in existence" - but it had not been disclosed.
"It would not be fair for Mr Lowery for the trial to continue," he said.
The Crown case is that the defendant became so frustrated that Rua the sea lion was stealing fish from his nets and ripping holes in them that he sought revenge.
Her body was found on a rocky beach at Quarantine Point on November 5, 2016 bearing two stab wounds.
Prosecutor Craig Power said the police seized a bayonet from Lowery's home, which was the weapon allegedly used.
He told the jury at the trial's outset that sea-lion and human DNA was found on the blade.
But the trial never got far enough for defence counsel Judith Ablett-Kerr QC to challenge that or other scientific evidence.
She said the police inquiry into Rua's death was defective from the start.
"Rather than a full and independent investigation that we would normally expect from the police, there was, in this particular instance, a bias; a fundamentally flawed investigation that focused its attention on only one man."
The matter will be called again in court next month.
Lowery's bail was varied so he was allowed to fish again.