"We are deeply concerned about the events in Sydney and the allegations to behead an innocent person for the glory of ISIL," said acting president Gary Ismail.

It was "patently un-Islamic and these people would be nothing more than murderous criminals and in violation of the tenets of lslam," Mr Ismail said.

Muslim leaders have urged Australians not to fear their peace-loving Muslim neighbours, as they set up a Facebook page to track incidents of religious hatred and discrimination.

In the wake of Thursday's counter-terrorism raids in Sydney and Brisbane, the Grand Mufti of Australia, Dr Ibrahim Abu Mohammad, released a statement to "reassure all Australians that they have nothing to fear from their Muslim neighbours who want peace and security for everyone regardless of religion".

"We have a vested interest in the safety and security of Australia," Dr Mohammad added.

The statement also said those arrested and charged in Thursday's raids must be afforded the presumption of innocence so the judicial process could take its course without prejudice.

Mr Ismail agreed, urging commentators to refrain from sensationalising the case.

Senior federal MPs have rejected claims made by a small group of protesters in western Sydney that Thursday's counter-terrorism raids were a conspiracy to attack Muslims.

"This certainly isn't any sort of conspiracy, this is based on intelligence work that's been going on over some time," Deputy Opposition Leader Tanya Plibersek said.

She said the vast bulk of Muslims in the community were patriotic Australians.

They were the country's best allies in the fight against extremism, she said.