Samier Dandan, the head of the Lebanese Muslim Association said the Muslim community is doing what it can to fight extremism, but with limited resources at its disposal.
Mr Dandan told a media conference in Sydney today that said ordinary Muslims are now being harassed in their daily lives because of the actions of a radicalised minority.
"Our concern, first and foremost, is security, as long as it doesn't infringe of civil rights of any citizen of this country," he said.
He said the solution to extremism among young Muslims lies with the whole community and should not just be seen as something for the Muslim community to deal with alone.
"We need to understand the cause root issue in its local context."
"This is not something that is seasonal, this is not something that is going to be resolved or finished tomorrow or the day after".
He also warned about responding to to fear with the removal of civil liberties or enacting laws that could be used to target minorities, widely interpreted to mean the Government's proposed new terror laws.
"It's about addressing the core values that we as Australians all adhere to". he said.
"I wouldn't say we need to sacrifice our freedom for the sake of security.
"We, as Australians, need to dictate what is proper for our way of life".
At the press conference the Grand Mufti of Australia, Dr Ibrahim Abu Mohammad, called on everyone to "exercise restraint and civility".
His words echoed by an executive member of the Australian National Imams Council, Sheik Yahya Safi.
"Sadly, in reaction to understandable fear some people have given in to abuse and victimising the innocent," Sheik Safi said.
"Community harmony should be maintained at all costs. We must not let emotions take over common sense. I call on categorical calm for all Australians."
The Grand Mufti also rejected the global fatwa issued by the self-proclaimed Islamic State, which mentions Australians.
It follows calls for calm by the Australian Federal Police and Victorian Premier Denis Napthine, who said the shooting was a tragic and isolated incident which should not be allowed to divide the community.
Dr Napthine says the incident is not about faith or ethnicity, but the alleged behaviour of one individual.
"It is critical that one particular group is not singled out or targeted."
Dr Napthine said the state had a harmonious, diverse multicultural and multi-faith community and "we shouldn't let a single incident divide that".
Attacks against Muslim community
The press conference began with a statement from a Muslim community spokeswoman, who described a number of incidents targeting members of the Muslim community over the past week.
"A number of women, particularly in hijab, and children have been verbally abused and threatened," she said.
"In one case a western Sydney mother and her baby were spat on and her pram kicked. In another, a man in Perth tried to rip the scarf off a woman's head.
"Several mosques around the country have been threatened, egged, vandalised and a pig's head impaled on a cross.
"A church and a Catholic school have also been the target of hate-crimes. Several incidents have been reported of property vandalised, including cars spray-painted with threatening messages."
The Secretary of the Islamic Council of Victoria, Ghaith Krayem, told Fairfax radio many people from an Islamic faith had felt "under siege" due to the public debate surrounding IS.
But he says the entire community can help put them at ease.
"One, be mindful of the language that we use generally," he said. "Two don't be scared when you see someone walking down the street with a headscarf or a long beard. They are no different from you are."