The Australian pilot - who sparked the Covid-19 scare onboard the Rio De La Plata - was last on the ship on 23 July.
Queensland health authorities believe the pilot caught the virus on the ship.
Chief Health Officer Dr Jeannette Young confirmed the pilot was fully vaccinated, which may have had an impact on the onset of symptoms.
He developed symptoms on 31 July, so health authorities initially believed he was infectious from 29 July.
That was why he was not picked up while authorities were contact tracing the case of the Cairns taxi driver.
Young said the pilot probably caught the virus on the ship, before passing it on to a taxi driver in Cairns.
The taxi driver had taken the pilot to the airport on 26 July.
That case put Cairns and Yarrabah into a snap three-day lockdown.
Genome sequencing has confirmed the two cases are linked.
Young said the pilot left the ship on 23 July so further contact tracing is underway.
"Now we've got this information from New Zealand about the ship that he piloted, he came off that ship on 23 July and we think that's probably where he acquired it. We're going to have to go back and contact trace to 23 July."