Federal frontbencher Christopher Pyne has rejected suggestions school prayer groups could be a "doorway" to extremism, saying prayer is a "good thing".
The industry minister, who was previously charge of the education portfolio, also said banning such groups would be counter-productive.
"I don't think prayer is the problem," Mr Pyne told Nine Network on Friday.
"Radicalisation is the problem and that's why, when I was education minister, I asked the state and territory ministers to join with me in a de-radicalisation program in schools."
"Let's not address the wrong issue, let's address the right issue."
The minister was backed by Labor frontbencher Anthony Albanese.
"We need to target, very effectively, that radicalisation because if we get distracted by other issues, we won't be as effective as we should be in targeting it," Mr Albanese said.
Three of the four males arrested in Wednesday's pre-dawn counter-terrorism raids in Sydney have since been released.
One, 18, remains in custody without charge after investigators applied for a court order extending his stay behind bars.
Some of those arrested had attended the same Parramatta mosque where 15-year-old Farhad Khalil Mohammad Jabar spent time before he shot and killed NSW Police accountant Curtis Cheng last Friday. Jabar himself was shot dead by police.
Mr Pyne denied Prime Minister Malcolm Turnbull had been "ducking and weaving" on the threat posed by extremist ideology in Australia the wake of Mr Cheng's murder, saying it was critical the government set the "tone right" in countering terrorism.
"We want Muslim communities to be onboard with the battle against terror. We don't want them to feel marginalised and go further to the edges. We want them to be in the centre," he said.
"Families, communities, mosques, Muslim leaders - we need them to be a part of our agenda.
"They're being maligned and smeared by the action of a few."
