ABC managing director Mark Scott has defended the national broadcaster as being "on the side of Australia", after Prime Minister Tony Abbott said "heads should roll" over Monday night's Q&A program.

The Federal Government has launched an investigation into the broadcaster's decision to allow Sydney man Zaky Mallah into the show's live studio audience to ask a question of Liberal MP Steve Ciobo.

Mr Mallah was found not guilty of preparing a suicide attack on a Commonwealth building after being held for two years in Goulburn jail, but in a plea bargain he pleaded guilty to threatening to kill ASIO officials.

He had also travelled to the war zone in Syria.

Mr Abbott has described Mr Mallah's appearance on Q&A as a betrayal and questioned "whose side" the ABC was on.

The ABC had already conceded it was an error of judgment and in a speech on Thursday night Mr Scott said the "risks and uncertainties of having [Mr Mallah] in a live programming environment weren't adequately considered".

But Mr Scott declared the ABC was on Australia's side.

"In any team, you can be playing on the same side, but often you will be playing in a different position, with a different role and responsibility," he said.

"You're on the same side, but with a different job to do.

"The ABC is clearly Australian, it's on the side of Australia."

This morning the ABC confirmed that security has been stepped up at the broadcaster's major offices across the country after a number of threatening phone calls were received.

Speaking at the event for the Centre for Corporate Public Affairs last night, Mr Scott described the media "firestorm" since Monday's Q&A as "ferocious".

"But even for the ABC, things seemed to have been taken to a new level when on Wednesday we scored four covers in one day in the News Limited tabloids, complete with photoshopped ABC flags being waved by jihadi protestors," he said.

"Not all parties to the conversation have seemed vested in pursuing rational discourse."

He also pointed out that some of these media outlets had themselves spoken to Mr Mallah in recent years.

"If giving him space or time to express his views is an act of sedition, then the round up of the seditious will take some time and include, I should add, The Australian newspaper which ran an extensive article on him in 2012, charting his journey from when terrorism charges were first laid against him," he said.

"He also graced the pages of The Courier-Mail."

'It's not weakness to say you made the wrong call'

However, Mr Scott said the live television format of Q&A meant there were additional risks with Mr Mallah's appearance.

"These things needed to have been thought through carefully and referred up internally," he said.

He acknowledged that some ABC staff had argued it was a sign of weakness for the broadcaster to admit it was wrong.

The Government's inquiry into Q&A will look at: The context in which Mr Mallah appeared on Q&A, including his previous engagement with the ABC

The context in which Mr Mallah appeared on Q&A, including his previous engagement with the ABC The decision-making process for Mr Mallah's appearance

The decision-making process for Mr Mallah's appearance The protocols that were used in regard to physical security for the live broadcast

The protocols that were used in regard to physical security for the live broadcast The decision-making process for the subsequent re-broadcast of the Q&A episode

The decision-making process for the subsequent re-broadcast of the Q&A episode The extent to which existing broadcasting codes apply to this situation

"Respectfully, I disagree," he said.

"It's not weakness to say you made the wrong call."

Mr Scott said at times ABC stories would frustrate politicians but it was the ABC's job to be independent.

"The ABC Act does not envisage the ABC as another branch of Government public relations," he said.

Communications Minister Malcolm Turnbull told 7.30 his department would conduct the Government's investigation into Q&A, looking at "what happened and who knew what, where and when".

He said he had discussed the matter with Mr Scott and with ABC chairman Jim Spigelman.

"This was a very, very grave error of judgment. And the management has to take responsibility for it, and that there should be consequences," he said.

"We are talking about a live audience on one of the most influential programs on the national broadcaster."

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 13 minutes 51 seconds 13 m Jonathan Holmes and Gerard Henderson debate the role of the ABC

He said the ABC had let down its own standards by rebroadcasting Monday's Q&A the next day.

The ABC said it would cooperate with the Government's inquiry into the program, which is due to report back next Tuesday, and the broadcaster is conducting its own review.

The ABC has received at least 1,000 complaints about the program, including threatening phone calls.

Switchboard operators at the national broadcaster have described some of the calls as "abusive" and "explicit".

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