The One Nation leader entered the Senate shortly after Question Time began on Thursday afternoon.
There were audible groans in the Senate as she entered and someone was heard saying "What on earth?"
It’s believed the President of the Senate had confirmed her identity before she entered.
Senator Hanson removed it a few minutes later as she attempted to ask a question to the Attorney-General on banning the burqa.
“There has been 13 foiled national threats against us with terrorism,” she told the Senate.
“Will the Attorney-General ban this burqa?”
Senator Brandis' passionate impromptu response to the One Nation senator's stunt earned a standing ovation from Labor and Greens senators.
“You are not an adherent of the Islamic faith,” Senator Brandis said in a passionate response.
“I would caution you and counsel you. Be very, very careful of the offence you may give.”
"We have about 500,000 Australians in this country of the Islamic faith. And the vast majority of them are law abiding good Australians."
Mr Brandis said that it was vital to work with the Muslim community to combat the threat of radicalisation.
"It is vital for their intelligence and law enforcement work that they work cooperatively with the Muslim community, and to ridicule that community, to drive it into a corner, to mock its religious garments is an appalling thing to do and I would ask you to reflect on what you have done."
Independent Derryn Hinch asked Senator Parry whether he could come into the chamber wearing fancy dress, given Senator Hanson is not a Muslim.
Senator Parry said he would not interfere with what Senators wore.
Senator Hanson will move a motion in parliament later on Thursday calling on the federal government to ban the burqa.
The stunt has drawn anger from the opposition benches, with crossbencher Derryn Hinch questioning whether Senator Hanson could remain in the chamber.
"I understand that she is not a Muslim, not of Islamic faith. Can I appear tomorrow in fancy dress unchallenged?" he asked the president.
NSW Muslim MP Jihad Dib said the incident was "calculated and divisive".
Former health minister Sussan Ley also weighed in on Twitter.
Independent senator Cory Bernardi also weighed in on the stunt.
"I did warn you that proroguing the parliament was in national interest. Things are getting seriously weirder by the day," he posted to Twitter.