“The team found the man hiding in the hull of the vessel,” NT Police Commander Matt Hollamby said.
“We thought this was a little bit suspicious and it turned out it was who we thought it was.”
Horne was on bail and charged with shooting a truck driver during a robbery at Lithgow in 2020 when he went on the run last October, sparking a nationwide manhunt.
The 32-year-old allegedly cut off his ankle bracelet in an Uber at Riverwood before chartering a plane from Bankstown airport to Queensland.
Horne had surrendered his passport as a condition for his bail, but police at the time believed he was planning on fleeing overseas.
He was taken into custody after his discovery.
Horne is expected to face an extradition hearing in Darwin on Monday before being flown back to Sydney by NSW Criminal group detectives.
Police also arrested two other men – one from Queensland, the other from the UK.
Both have been charged with trying to help the fugitive escape the country.