Four men have now been arrested as part of the counter-terror raids, which saw more than 800 state and federal police officers carry out operations across a dozen Sydney suburbs on Thursday.
The raids sparked a backlash from the Muslim community, prompting Mr Abbott is call for calm.
He urged Australians to remember the raids were about crime, not religion.
“The police actions yesterday were about crime,” he said.
“They weren't about any particular religion or any particular community.”
'The vast majority of Australian Muslims are absolutely first class Australians'
Speaking to Channel Seven and Nine on Friday, Mr Abbott also addressed the protest against the raids.
Hundreds of protesters rallied in Lakemba on Thursday night to highlight “government aggression” against the Muslim community, but Mr Abbott dismissed the action as “quite small”
“The vast majority of Australian Muslims are absolutely first class Australians,” he said.
The event was promoted under a banner featuring the hardline organisation Hizb Ut-Tahrir and is calling on the Muslim community to "stand as one" against "government aggression".
"Women, children should be safe from the terror of the state," they chanted.
The signs had small Hizb Ut-Tahrir Australia logos.
Speaking later on Friday, Mr Abbott said he did not want to isolate the Muslim community.
"I want to wrap up the extended family of Australia in an embrace," he said.
"We're all in this together."
Bernardi ‘out of line’ on burqa comment
The action also followed comments by Liberal Senator Cory Bernadi, who highlighted that some people impacted by the raids were wearing burqas.
The controversial tweet, slammed by both Mr Abbott and Opposition Leader Bill Shorten, stated that the burqa was a “shroud of oppression” that is not right for Australia.
Mr Abbott dismissed the comment, stating that the raids were not about religion or clothing, while Mr Shorten gave a heavy critique of Senator Bernardi’s comments on Thursday.
Mr Shorten said Senator Bernadi should not be fuelling suspicion.
"Why on earth is this out of touch, out of line senator on a rampage with his ignorant and stupid comment?" he said.
"I was so frustrated and angry by those ignorant comments... I'm not sure that's totally helpful."
Parliament House a target
Mr Abbott also confirmed that security had been strengthened at Parliament House as a result of the raids.
Confirming reports that there are concerns that he and other senior officials could be targeted, Mr Abbott said Australian Federal Police officers had been redeployed to the iconic Canberra building.
He said a review of security had also been undertaken.
“Parliament House certainly is a potential target,” he said.
“There has been chatter about this for some time.”
Mr Abbott also failed to rule out more raids in coming days and weeks, saying that Australia was in “a heightened state of vigilance”.
He said for an ISIS attack to occur, "all you need is a determined individual.... a knife, an iphone and a victim”.
“It's difficult to entirely protect our community from this kind of act,” he said.
