Detectives have raided the Ruby Princess cruise ship to seize its black box and question crew members about the docking and disembarkation of passengers in Sydney three weeks ago.

The vessel has been linked to hundreds of Covid-19 cases and more than a dozen deaths across Australia.

NSW detectives wearing personal protective equipment boarded the vessel at Port Kembla on Wednesday night to gather evidence about how hundreds of passengers aboard were allowed to leave the ship on 19 March.

“Strike Force Bast investigators are conducting inquiries on-board the Ruby Princess this evening,” NSW Police said in a statement.

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

The NSW police commissioner, Mick Fuller, said officers seized a black box “very similar to that of international planes” and other evidence. He said the ship’s captain had been extremely helpful.

Fuller also said the majority of the ship’s crew wanted to remain on the ship, which he described as a “good outcome”.

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

“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.”

He said people had dropped off a number of care packages at the port for the crew members, “which I think speaks volumes for the local community”.

In coming days police will interview other high-priority witnesses about the scandal, while the vessel is expected to remain at Port Kembla for 10 days with 1,040 crew members undergoing medical assessments.

Police prepare to raid the Ruby Princess in Port Kembla on Wednesday evening. Photograph: Nathan Patterson/NEW SOUTH WALES POLICE/AFP via Getty Images

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

Questions remain over who is responsible for the Ruby Princess fiasco.

The Australian Border Force confirmed overnight it had been engaged in discussions with the Port Authority about the Ruby Princess before it docked in Sydney.

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

The ABF said on Wednesday 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.

The Sydney Morning Herald and the Age have reported that an ABF officer told a Sydney harbour master to allow the ship to dock.

Meanwhile, new Covid-19 infections continue to stabilise with NSW recording only 39 new cases on Thursday, taking the state’s total to 2,773.

There are 31 people in intensive care and the death toll remains at 21.

The premier, Gladys Berejiklian, welcomed the stabilisation and decline of new cases but warned community transmission was still increasing.

She said that while social distancing would be necessary until a coronavirus vaccine or cure is found, restrictions are being reviewed on a month-by-month basis.

She reminded people to adhere to restrictions, which are having a positive effect, as authorities keep a watchful eye on increasing community transmission.

NSW Health says there are 36 travellers currently in hotel quarantine who have tested positive to Covid-19, and 121 quarantined travellers showing coronavirus symptoms.

The first group of 288 Australians quarantined at the Swissotel in Sydney’s CBD were released on Wednesday morning, with police planning for further departures when some 3,000 Australian residents are expected to leave hotel isolation over the next week.