The men remain in custody following weekend raids across Sydney, prompted by the discovery of the alleged conspiracy to down a Gulf-bound aircraft.
Mr Fuller on Thursday said the reasons for the police action would become clearer in the coming days.
"As this matter progresses, and in my opinion people will be charged, and the facts are tendered, you will understand about the police operation more holistically," he told reporters in Sydney.
"Australian Federal Police have the lead in the matter but, from my perspective, the evidence gathered is very strong."
A fourth man, 50-year-old Abdul Merhi, was also arrested on Saturday but released without charge on Tuesday evening.
Mr Fuller said he "absolutely disagreed" with suggestions Mr Merhi should never have been detained.
"Terrorism is very different to other crimes," the commissioner said.
"You can't wait until you have all the pieces of the puzzle because you can't afford to let the criminal act happen."
Mr Merhi's solicitor, Moustafa Kheir, wants to review "what basis police had to do what they did".
Kheir tweeted on Wednesday that "it's just unfathomable" that his client would be associated with anything like this.
Mr Fuller welcomes that scrutiny.
"Oversight and people reviewing police action is totally fine," he said.
"But at the same time I've got the challenge of protecting the people of NSW.
"I've been given strong powers, strong legislation, I'll use those."
Investigators have combed through homes in Lakemba, Wiley Park, Punchbowl and Surry Hills, and Mr Fuller said the searches were forensic.
"This would be the most detailed type of search that we would do for any crime in NSW."
One theory is that the group intended to use a meat grinder as a vessel for explosive chemicals.
Police can hold the three remaining suspects until at least Sunday evening without charge under powerful terror legislation.
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