La Trobe University could soon face legal action over its treatment of Safe Schools Coalition co-founder Roz Ward, who it suspended for calling the Australian flag "racist".

National Tertiary Education Union Victorian Secretary Colin Long said the union will write to La Trobe demanding that it reinstate Ms Ward and drop misconduct charges..

If it does not, the union will launch legal proceedings on Monday.

"We are determined to take all possible legal actions to defend Roz and get her back to work, and to defend the fundamental principle of free speech," he said.

He said La Trobe University had breached the Fair Work Act and human rights laws.

The move to stand down the controversial figure from the university's Australian Research Centre in Sex, Health and Society has been condemned by academics, while a petition in support of Ms Ward has already gathered more than 3000 signatures.

La Trobe University said on Thursday that it was following disciplinary processes and no decision had been made about Ms Ward's future.

A spokesman said the university valued independent thought and academic freedom.

Australian Lawyers Alliance spokesman Greg Barnes said La Trobe University appeared to have breached Victoria's charter of human rights, which says people have a right to political communication and freedom of speech.

"I cannot think of any justification as to why a university would suspend an employee who simply makes an assertion that millions of other Australians would also make," he said.

"She is not inciting violence, engaging in discriminatory conduct or race hate. There are millions of Australians who think we should have a new flag."

He said the move sent a chilling message to academics.

On Wednesday, university management told Ms Ward that she had been suspended from work for "engaging in misconduct". It followed Ms Ward posting a photo of the rainbow flag on her Facebook page last week, along with the words "Now we just need to get rid of the racist Australian flag on top of state parliament and get a red one up there and my work is done".

Maurice Blackburn employment lawyer Josh Bornstein said employers who disciplined or sacked an employee based on an expression of a political view could be in breach of the Fair Work Act. 

La Trobe University academic Bianca Fileborn, who works with Ms Ward at the Australian Research Centre in Sex, Health and Society, said she was "absolutely appalled and shocked" by the university's action over a private Facebook post. 

Victoria University law lecturer Su Robertson said that freedom of expression was "central to being an academic". 

The Victorian government said on Thursday that it played no part in the university's decision.

"This is an individual employment matter for Roz Ward and La trobe University - the government had no part in the decision," a spokeswoman said.

The government reiterated its support of Safe Schools, an anti-bullying program that promotes the acceptance of LGBTI people and runs out of La Trobe University. It will become mandatory in all Victorian state secondary schools by 2018.

The National Union of Students said it was unfair for someone to lose their job over personal political views posted on a private Facebook feed.

Members of the LGBTI community have come out in support on a Facebook group called We Stand With Roz Ward.

Meagan Michelle said Ms Ward was supportive of her family when her daughter was transitioning at a Christian school.

"She supported us over a period of our lives that was one of the most difficult, and not once in that time did she ever not be a professional," she said on the I Stand With Roz Ward Facebook page.

Matthew Lesh, a research fellow at right wing think tank the Institute of Public Affairs said the university had set a "dreadful precedent".

"I fundamentally disagree with her sentiments, however I stand stead-fast in supporting her freedom of speech," he said. 

The hashtag #IstandwithRozWard was also trending on Twitter on Wednesday night.

Transgender student, Erik Ly, tweeted his support for Ms Ward.

A T-shirt calling for Ms Ward to stay at La Trobe has also been launched online for sale.

Jo Hirst, author of The Gender Fairy also came out in support of the academic.

Southern Cross University's emeritus professor James Jackson, an expert on academic freedom, said Australian universities traditionally stood by academics who expressed controversial and unpopular views.

He said the suspension was unjustified, and referred to a clause in the La Trobe University Act, which states that the university strives to promote "critical and free enquiry, informed intellectual discourse and public debate within the University and in the wider society".

He said Ms Ward's claim that the Australian flag was racist may not be popular, but it would trigger a worthwhile debate.

This is not the first time academics have been sanctioned for expressing provocative views.

• In the 1930s, Sydney University's Professor John Anderson opposed building the war memorials after the First World War and opposed organised religion. Politicians called for his dismissal, and while he was censured by the university senate, he was not stood down.
• In 2001, Professor Ted Steele was dismissed by the University of Wollongong after he complained about soft marking and lower standards, especially for full-fee-paying foreign students.
• University of Melbourne demoted  transport and planning expert Professor Paul Mees in 2008 after he criticised Victorian government transport officials.
• Professor Barry Spurr was suspended by the University of Sydney in 2014 over leaked racist emails that were published by a news website.