Clad in protective gear, officers boarded the Ruby Princess cruise ship in Port Kembla, south of Sydney on Wednesday night to seize evidence.
About 2,700 passengers disembarked from the vessel on March 19 in Sydney - since then, the boat has become the largest source of Covid-19 infections in Australia.
New South Wales Police said the Ruby Princess was expected to remain in port for 10 days while its 1,040 strong crew undergo medical assessments.
About 200 crew members have shown symptoms of coronavirus, while 18 have tested positive for the virus.
The more than 1,000 workers still on board are nationals from 50 different countries.
New South Wales Police Commissioner Mick Fuller said on Thursday that officers seized a black box "very similar to that of international planes" and other evidence.
The police commissioner said the captain had been extremely helpful and added: "I can confirm there’s still over 1,000 crew members on the ship."
He said that three-quarters of staff wanted to remain on the ship.
"They feel safe on the ship and I think that's a good outcome."
On Thursday, Australia recorded its lowest increase in coronavirus cases in more than three weeks.
As at 9am on April 9, 2020, a total of 6,052 confirmed Covid-19 cases, including 50 deaths, were reported.
Health Minister Greg Hunt said there were 96 new cases reported overnight, the first time there have been fewer than 100 new positive tests a day since March 17.
The peak in Australia was on March 28, when 457 cases were recorded.
Seeking to limit the impact on the economy, politicians passed a wage subsidy programme late on Wednesday worth 130 billion Australian dollars.