The besieged Ruby Princess will be the lone cruise ship left in Sydney after Sunday, as health authorities, police and Border Force grapple with what to do with the ship and its crew and NSW Police Commissioner Mick Fuller launches an investigation into the disastrous decision to allow its passengers to disembark.

The "hours leading up to the ship coming in" will be key to the police investigation, Commissioner Fuller said.

"There will be documentation, triple 0 calls, there will be evidence, hard evidence, that will help me work out which direction to take it," he said on Friday morning, saying it was too early to know whether criminal charges could be laid.

The ship continues to languish off Port Botany because of an outbreak of respiratory disease among the 1200 crew, and there are no immediate plans for it to leave.