A handful of Muslim leaders refused to attend talks with the government this week in Melbourne and Sydney, where Mr Abbott pitched security laws aimed at radicalised Australians.
Their response disappointed the prime minister who says he wants everyone on "Team Australia".
"You can hardly complain that people aren't talking to you and when you offer them to talk say `sorry we're not coming'," he told ABC radio on Thursday.
Laws are being drafted that would, among other measures, require telcos to keep metadata information on calls and internet use, and reverse the onus of proof by deeming a person guilty of an offence if they travel to certain locations overseas.
While some Muslin leaders "rather foolishly boycotted" the talks, there was a "Team Australia" spirit among those who did attend, Mr Abbott said.
"One of them was even good enough to say, we are all part of Team Australia and you are our captain.
"Although, I imagine from time to time he might have wanted a different captain."
Not everyone at the meetings agreed with the government's policy, Mr Abbott said.
Some Muslim groups have dismissed the planned laws as a response to a "trumped-up threat".
While the official terror threat level hasn't changed, the government is concerned about Australians engaging with terrorist organisations overseas.
About 150 Australians have been directly linked to conflicts in the Middle East with 60 known to be fighting in Syria or Iraq where Islamic extremists have been involved in brutal incidents.
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