The world champion kayaker and his younger brother Dru Baggaley were each found guilty in 2021 of attempting to import up to $200 million worth of cocaine.
Nathan Baggaley represented himself in arguing in the Queensland Appeal Court on Thursday he should receive a sentence of "eight years top" rather than 25 years behind bars.
Dru Baggaley, who was jailed for 28 years, also appealed his sentence during earlier proceedings.
After the jury's verdicts, Brisbane Supreme Court Justice Ann Lyons found Dru Baggaley to be "a principal organiser" of the plot and recruiter of another man Anthony Draper to go to sea with him.
Draper and Dru Baggaley set off on a rigid-hulled inflatable boat (RHIB) from Brunswick Heads in July 2018, meeting a foreign freighter about 360km off Queensland's coast about 11 hours later.
The men retrieved packages thrown off the other ship, but on their return flung them into the sea when pursued by an Australian navy vessel.
Bundles recovered at the time, together with those that washed ashore for months after, had 650 kilograms of white powder containing cocaine worth between $130 million and $200 million.
The two men were arrested before they reached shore and Nathan Baggaley - found by Justice Lyons to be "actively involved" in the attempted importation - was taken into custody almost a year later.
A phone found on the RHIB had partially readable messages sent via the Threema application from the username "Thunderbutt" stating "How's things" and "I'm on standby ready", the trial heard.
When police searched Nathan Baggaley's northern NSW home days after his brother's arrest he did not comply with an order to unlock one phone that contained encrypted messaging apps.
An old phone had the Threema app but the user name was "Big Boy", Nathan Baggaley told the Appeal Court.
"It was not and could not be suggested it was 'Thunderbutt'."
He said there was no suggestion that phone was involved in the importation plot.
"There was no evidence in the trial that 'Big Boy' (has) done anything.
"That's where I have an issue with Her Honour … she has found me to be 'Thunderbutt' on that phone."
Justice Lyons found the only reasonable conclusion was that the message was sent by Nathan Baggaley given his phone contained the messaging app and he failed to provide police access to the app on his phone.
"Clearly then given that Nathan is asking for an update and is on standby to assist he must have known that there was a plan to import a consignment of something," she said.
"He would not have needed to be on standby if there was no cargo."
But Nathan Baggaley said if the "Thunderbutt fact" was removed, Justice Lyons would have struggled to reach that conclusion.
Asked about his fingerprints on tape covering the boat's registration Nathan Baggaley said there were many possible reasons for that.
"It's not just automatically an importation of border controlled drugs," he added.
The crown case was that Nathan Baggaley bought the boat and trailer and was at Brunswick Heads ready to receive the consignment when the RHIB was expected to return.
"It would seem really implausible to me that 'Thunderbutt' would be sitting there waiting," Nathan Baggaley said.
Dru Baggaley will not be eligible to apply for parole until he has served 16 years, while Nathan has a 12 year non-parole period of imprisonment.
The Appeal Court will deliver its judgment on a date yet to be set.
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