Mr Walker's report says NSW Health should have ensured ships were aware of the change to the definition of a "suspect case" for COVID-19 made nine days before the ship docked in Sydney.
"This would have resulted in the identification of such cases on the Ruby Princess 101 persons fell within the suspect case definition by March 18, and 120 by the time the ship docked," it says.
"NSW Health should also have ensured that such persons were isolated in cabins. These were serious mistakes by NSW Health."
The report also warned that the failure to ensure swabs were collected by an on-board health assessment team "was a serious failure by NSW Health".
Mr Walker describes the delay in obtaining test results for the swabs taken from the Ruby Princess on the morning of March 19 as "inexcusable".
"Those swabs should have been tested immediately," he wrote in his report.
One of Mr Walker's harshest criticisms was also directed at the federal government.
Mr Walker said many people were of "great assistance" during the inquiry, including the NSW Police Commissioner, but said the "one fly in the ointment ... is the stance of the Commonwealth".
"A summons to a Commonwealth officer to attend and give evidence about the grant of pratique for the Ruby Princess was met with steps towards proceedings in the High Court of Australia," the report says.
"Quite how this met the Prime Ministers early assurance of full co-operation with the commission escapes me."
The report also highlights the state government's failure to have arranged "suitable accommodation for all passengers" after they disembarked who were not residents of NSW.
"The directive to allow passengers to onward travel interstate and internationally after disembarkation on March 19 did not appropriately contemplate or comply with the terms of the Public Health Order that came into effect on March 17," the report notes.
The health order required all cruise ship passengers entering the state from any other country to isolate themselves "in suitable accommodation for 14 days".
It also said passengers were initially given the wrong information about self-isolation.
"Passengers were incorrectly advised by the ABF [Australian Border Force] during the cruise that their 14-day period of self-isolation would commence from the date of departure from the last overseas port visited by the Ruby Princess, being Napier on March 15," the report says.
"This inaccuracy was later clarified during disembarkation at the Overseas Passenger Terminal on March 19, when passengers were provided with a fact sheet published by the Commonwealth Department of Health which relevantly instructed them to self-isolate for 14 days from their arrival in Sydney."
But Mr Walker said a fact sheet linked to an email sent to passengers at 10.46am on March 20 wrongly advised that they were allowed to continue with onward travel, despite being identified as "close contacts" of a confirmed COVID-19 case.
"Although this advice was corrected by NSW Health by the evening of March 21, it was at that stage too late to prevent a considerable number of interstate and international passengers from onward travelling, including some passengers who were symptomatic during transit," Mr Walker wrote.
But Mr Walker stressed that despite a range of serious mistakes by NSW Health, there were no "systemic" failures to address.
"The mistakes made by NSW Health public health physicians were not made here because they failed to treat the threat of COVID-19 seriously," Mr Walker wrote.
"They were not made because they were disorganised, or did not have proper processes in place to develop a plan to assess the risks posed by this disease, and how to limit those risks.
"Those physicians relied on the best science, not pseudo-science or matters of political convenience. They were diligent, and properly organised.
"Put simply, despite the best efforts of all, some serious mistakes were made."
Premier Gladys Berejiklian said she would be making more detailed comments next week.
"In the public interest and for full transparency I am releasing it immediately," she said.
"I have just received the report. I will read it over the weekend and respond early next week.
Mr Walker defended his decision not to call NSW Health Minister Brad Hazzard to appear before the inquiry and said calls for Mr Hazzard's resignation were unnecessary.
NSW Labor repeatedly called for Mr Hazzard to step down in the weeks after the cruise ship debacle.
"Of course a minister should resign in some circumstances, but as this commission sees it, without wading into the partisan politics, this case would not appear to fit that outcome," Mr Walker wrote.
"The failures were professional failures in decision-making by experts. They are not, as to their expert judgments, subject to ministerial direction. Nor should they be, unless our system of government were to become farcical."
In a statement from Princess Cruises, which is owned by Carnival Corporation, it said "our hearts go out to everyone who has been affected, particularly those who lost loved ones".
"The commissions report confirms that none of our people the captain, the ships doctor, or members of our shoreside port agency teams misled public authorities involved in Ruby Princess being permitted to disembark guests on March 19," the statement said.
"We acknowledge the commissions specific comments about Carnival and we will consider these comments to the fullest possible extent."
One of the criticisms of Carnival was that it should have ensured that the ship's doctor Ilse von Watzdorf was made aware of the change to the definition of a "suspect case".
"They should also have ensured that passengers and crew aboard the Ruby Princess were informed that there were suspect cases of COVID-19 on board. Those persons meeting the definition of a suspect case should have been required to isolate in their cabins," the report says.
NSW Labor leader Jodi McKay said the opposition was the first to call for the special commission of inquiry and Ms Berejiklian should "issue a sincere apology for these serious failings".
"We maintained from the beginning that the failings of the NSW government led to this major public health crisis," Ms McKay said.