"I won't be cowered down to bullies like yourself."
Yesterday, Julia Gillard has dismissed as "stupid and wrong" Mr Bracken's belief.
The Federal Opposition seized on the comments in Parliament, with Victorian MP Josh Frydenberg asking Ms Gillard what action she would take against Mr Bracken “to send a message that such remarks are unacceptable”, The Australian reported.
“Obviously I don’t agree with the remarks, obviously they are stupid and wrong,” Ms Gillard said.
“The Labor Party is a large organisation, people join it as individuals – we don’t dictate what people think.”
After being accused by Liberal frontbencher Christopher Pyne of not answering the question on discipline, Ms Gillard said: “If it is the intention of the Leader of the Opposition to expel every member who says something stupid, I’ll start sending him a weekly list.”
In Victoria, Shadow Attorney General Robert Clarke said Mr Bracken's comments were a direct insult to Australian soldiers serving in Afghanistan.
"It strikes at the very heart of the West's struggle against terrorism and it is a disgrace that while Australian soldiers are serving and dying in Afghanistan that Mr Bracken make these wild claims that undermine the very reason for their presence in Afghanistan," he said.
Mr Clarke called on Premier John Brumby to condemn these comments in the strongest possible terms and for the outspoken union leader to be disciplined.
"The Trades Hall Council needs to consider Mr Bracken's future as its president and the MUA needs to consider his future as their secretary,'' he said.
"These comments can't stand they need to be condemned in the strongest possible terms.''
Trades Hall secretary Brian Boyd said Mr Bracken did not speak on behalf of the organisation.
"The official Trades Hall position is not to entertain that theory," Mr Boyd said.
"We had almost 3000 working people killed in that terrorist attack. It was a terrorist attack, and we condemn it."
Mr Boyd said Mr Bracken's views had caused many debates behind the walls of Trade Hall.
"He is welcome to his views and we've discussed his theories," he said.
"But I totally disagree."
Mr Boyd said he stood by his colleague despite his extremist views.
"99 per cent of the time Kevin's a very good president," he said.
MUA national secretary Paddy Crumlin distanced the union from the comment, releasing a statement saying its position on the attack was "unambiguous".
"The 9/11 tragedy was a result of a terrorist attack by international terrorists who claimed responsibility," he said.
"It is the MUA's position - one that I passionately support as national secretary - that this attack is one of the greatest affronts and abuses of human and civil rights in contemporary history."
This is not the first time Mr Bracken has voiced his controversial opinions on the attacks on the World Trade Centre and Pentagon.
In 2006 he told The Australian he believed the attacks only worked because the US Government was in some way involved.
"If they want to stop terrorism they've got to look at who was really behind September 11," Mr Bracken said at the time.
"It couldn't have happened unless there was participation from key elements of the American military and government and security services. I am not saying the whole lot were involved. But I believe the official story for September 11 doesn't stack up."
Mr Bracken said in 2006 his views on the terror laws and September 11 were his own, and he was not speaking on behalf of the union.