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Mr Fuller told a press conference on Friday that police had already detained 60 people from last week's protests and issued more than 200 infringement notices.
The commissioner said after monitoring online activity, police had to "expect there's going to be a protest".
"Please don't come into Sydney tomorrow to protest. If you do, you will be met by up to 1000 police who will be ready to deal with you, whether that be via the health orders or other laws," Mr Fuller warned.
The warning comes as NSW reported 170 new locally acquired cases of Covid-19 today. At least 52 of those people were circulating in the community for all or part of their infectious period.
The state recorded a record 239 local virus cases in the previous 24-hour period.
"Today's number is considerably less than yesterday ... We expect to see those numbers bounce around and what we do need (to see) is not just the stabilisation but of course the numbers to go down," Premier Gladys Berejiklian told reporters on Friday.
Meanwhile, NSW Chief Medical Officer Kerry Chant said authorities were still investigating whether a Covid-positive person had attended last Saturday's protest, which saw thousands march through Sydney's CBD demonstrating against the state's lockdown laws.
"We're just working with police to ascertain whether that person did attend. The police did indicate they had turned the person around and they had given an infringement notice," Dr Chant told reporters.
NSW Health Minister Brad Hazzard said if the Covid-positive man had attended the rally, "he was effectively carrying a deadly weapon, he was carrying the virus".
Dr Chant said investigations were still under way to work out whether any of the new NSW cases could be linked to the protest.
"People may not be open that they attended the protest. I am not aware of any cases that have arisen from the protest but many people may choose not to disclose that," Dr Chant said.
"I am totally committed to the fact that we need to have low tolerance for where people are flagrantly breaking the rule - this is too much of a severe disease, too serious a situation to be in, to have people knowingly going out when they are positive," she told reporters.
A NSW Police strike force was set up following last week's protests with up to 20,000 tip-offs to Crime Stoppers about attendees, with photos and names sent to police.
On Friday Mr Fuller said police will be waiting for anyone planning to protest this weekend, and they had been given plenty of warnings.
Mr Hazzard had his own warning.
"You have to be crackers to go to that demonstration tomorrow because there will be a lot of people potentially with a deadly weapon, Delta virus," Mr Hazzard said.
NSW Premier Gladys Berejiklian told would-be protesters, "your actions will hurt".
"Do not give those you love the most a death sentence," she said.