Australian police have raided the coronavirus-stricken Ruby Princess cruise ship – the country’s biggest single source of Covid-19 cases – and seized its black box as part of efforts to investigate the disembarkation of infected passengers in Sydney.

At least 15 deaths and hundreds of cases in Australia have been linked to the ship, which was boarded by detectives wearing personal protective equipment on Wednesday night.

“Police officers entered the Ruby Princess to gather evidence ... ships have a black box very similar to international planes and that and other evidence has been seized,” New South Wales Police commissioner Mick Fuller said on Thursday.

“The operation is being conducted under the strictest health and workplace safety guidelines.”

Key crew members are also being questioned, including the captain.

Authorities are working to establish who is at fault after the cruise ship’s 2,700 passengers were allowed to disembark on 19 March, despite some exhibiting flu-like symptoms.

After three more weeks at sea, the Ruby Princess docked on Monday at Port Kembla, 50 miles south of Sydney, to allow doctors to assess sick crew members and take the most serious cases ashore for medical treatment.

About 200 crew members have shown symptoms of coronavirus, while 18 have so far tested positive, according to authorities.

The majority of the ship’s crew is still onboard, with the vessel expected to remain in port for 10 days, Mr Fuller confirmed.

“I can confirm there’s still over 1,000 crew members on the ship. We’re working closely with [the ship’s owners] Carnival,” he said.

“Three-quarters at this stage say they want to remain on the ship. They feel safe on the ship and I think that’s a good outcome.”

Care packages have been delivered to the port for those quarantined on the ship, Mr Fuller said, adding that it “speaks volumes for the local community”.

The investigation into Carnival Australia will focus on communications and actions that led to the docking and disembarking of the ship’s passengers to see whether national biosecurity laws or state laws were broken, according to NSW Police.

State health authorities had classified the ship as low risk because it had sailed from Sydney to New Zealand, while the Australian Border Force (ABF) issued a notice allowing the passengers to travel home freely. They were required to self-isolate for 14 days.

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The ABF said it had received a call from the NSW Port Authority hours before the vessel’s docking, in which “concern” was expressed about the health of the passengers.

Despite this, the ABF claimed that NSW Health had cleared the ship to dock.

“The ABF officer made internal enquiries and subsequently advised the NSW Port Authority that the vessel had been cleared by NSW Health,” the agency said in a statement.

Carnival Australia said on Monday that the company would cooperate with the probe.

“In addition to willingly participating in the investigation, Carnival Australia will vigorously respond to any allegations of which there must now be full disclosure and the basis for them,” a spokesman said.

On Thursday, Australia recorded its lowest increase in coronavirus cases in more than three weeks.

Health minister Greg Hunt said there were 96 new cases, the first time there have been fewer than 100 a day since 17 March.

The peak was on March 28, when 457 cases were recorded.

“We are seeing some early positive signs as a result of the restrictions we’re putting in place,” NSW premier Gladys Berejiklian told reporters earlier this week.

As of Thursday, Australia had recorded just over 6,000 cases and 50 deaths, according to figures from Johns Hopkins University.