Two men who had planned to carry out a Christmas terrorist attack in Melbourne's CBD in 2016 have been found guilty of further terrorism charges.

Key points: The jury found the three men were motivated by an ideological cause

The jury found the three men were motivated by an ideological cause Two of the men were also found guilty of attempting to light a fire at the mosque a month earlier

Two of the men were also found guilty of attempting to light a fire at the mosque a month earlier One of the men yelled insults across the court at police

Ahmed Mohamed, 26, and Abdullah Chaarani, 28, were today found guilty of torching the Imam Ali Islamic Centre in December 2016, just weeks before they were picked up for the Christmas terrorist plot.

The pair had bought machetes and material to make explosives, and carried out reconnaissance at Federation Square, before they were convicted of the plot last year.

Today, the Supreme Court in Melbourne found the pair and a third man, Hatim Moukhaiber, 30, guilty of terrorism charges for burning down the Shia mosque in Fawkner, in the city's north, causing $1.5 million damage.

After two days of deliberating, the jury of six men and six women also found Mohamed and Chaarani guilty of an earlier failed attempt to torch the centre on November 25, 2016.

A court order had previously prevented the ABC from revealing the men's involvement in the Christmas terrorism plot while they were on trial for setting fire to the mosque.

Jury, police abused in court

The court heard the Sunni men had caused property damage to advance an ideological cause to intimidate a section of the public, which met the definition of terrorism, according to prosecutors.

There were emotional scenes after the verdict was read, as family members of the three accused reacted.

An older woman cried at the jury, before being told to leave the court.

"What are you doing? You dogs," she shouted.

Moukhaiber also yelled across the court to police, calling them "oppressors" and "dogs".

The fire at the Shia mosque in Fawkner in Melbourne's north happened in December 2016. ( ABC News: Rudy De Santis )

Later Moukhaiber's lawyer Felicity Gerry apologised to the court for her client's outburst, which she said happened when he saw the response of his mother and wife.

"Seeing them distressed caused him to react," Ms Gerry said.

As the jury was discharged, Mohamed shouted at them.

"Bye jury," he said, despite being asked to stop by Justice Andrew Tinney.

An extreme brand of Sunni Islam

During the five-week trial, the jury heard the men were opposed to Shia Muslims and wanted to intimidate the members at the Shia mosque.

"The accused were adherents to an extreme brand of Sunni Islam," prosecutor Nicholas Robinson said.

He said they shared "the same ideology as Islamic State."

The jury was shown security camera vision which showed three men arriving at the mosque, on Lowson Street, at about 2:30am on December 11.

Two men are seen inside the mosque — one carrying a container of fuel, another carrying two car tyres — before smoke is seen in the video.

The prosecution claimed Chaarani spray-painted the words Islamic State in English and Arabic on the walls of the mosque.

Chaarani's lawyer, Patrick Tehan QC, admitted his client did burn down the mosque in a "despicable act" but argued it was not a terrorist act.

The words Islamic State were spray-painted in English and Arabic on the mosque's wall. ( ABC News )

Instead, Mr Tehan said it was an act of protest, dissent or advocacy, which under the law did not constitute terrorism.

He likened it to animal rights activists causing damage while targeting a chicken farm.

"His act is criminal. His act is arson," Mr Tehan said.

"It is not a terrorist act."

But the prosecutor urged the jury to reject that and said the men acted with the aim of "destruction and fear".

"It is an affront to common sense that this act is any form of advocacy or any form of protest," Mr Robinson said.

"To burn down a religious institution because you think it's not right — whatever may be protest, that's not it."

Jihadist pictures found on phones

During the trial, the jury heard detailed evidence about text messages, WhatsApp conversations, telephone intercepts and other covert recordings, which the prosecution said showed the three men were in close contact before and after the arson attack.

The court also heard a jerry can containing petrol was found by police during a search of Mohamed's home when the men were arrested more than a week later.

A police tracking device attached to Mohamed's car recorded a number of trips past the mosque in the days after the attack.

But his lawyer, John Kelly, told the jury it was natural that a fire at a mosque would be "newsworthy" in the Muslim community.

"It's going to draw attention and curiosity — that's all that is explained by … Mr Mohamed driving past, looking at it," Mr Kelly said.

There was also evidence from police technical experts about images of extremist material on phones seized from the men, including images of jihadists in Iraq and Syria.

The men were caught on CCTV arriving at the mosque before the fire started. ( ABC News: Iskhandar Razak )

From the outset, Moukhaiber's lawyer told the court her client was not at the mosque on December 11, and that there were "a dozen or more other men who ought to be of interest to you" with large builds, shaven heads and beards like Moukhaiber's.

Ms Gerry also suggested the third man may have been a disgruntled member of the Shia community.

She pointed to the "police error on identification", where police had initially incorrectly claimed Moukhaiber was with Mohamed during a late night visit to a department store in Broadmeadows a few days after the attack.

The court heard Mohamed's hatred for Shia Muslims extended to the way he treated a fellow construction worker who was a Shia, by "getting him to do the asbestos jobs".

Justice Tinney will sentence Mohamed, Chaarani and Moukhaiber at a later date.