Jurors have begun deliberating in a terror trial against three men accused of spraying the words "Islamic State" on the Imam Ali Islamic Centre at Fawkner before setting it on fire in December 2016.

Abdullah Chaarani, Ahmed Mohmed and Hatim Moukhaiber are charged with committing a terrorist act against the mosque, substantially destroying it on December 11.

Chaarani and Mohamed are also charged with attempting to commit a terrorist act over what prosecutors allege was a failed first attempt on November 25.

Mohamed and Moukhaiber both deny any involvement in the attacks and deny it's them in CCTV footage.

Chaarani's barrister Patrick Tehan QC has admitted his client was there both times and was to blame for the fire.

But Chaarani argued it was an act of protest, advocacy or dissent, and not terrorism.

"He admits through us, his counsel, that he did so with the intention of advancing a political, religious or ideological cause, namely the advancement of Sunni Islam," Mr Tehan said.

Prosecutor Nicholas Robinson QC argued it was terrorism because the Shia mosque was targeted to intimidate Shia muslims.

It's alleged Chaarani and Mohamed tried to set fire to rugs and drapes with petrol on November 25, but the fire self-extinguished.

Mr Robinson argued all three men returned on December 11 with an almost-full 20-litre container of petrol and two tyres to "make sure it kept going".

"They tried to set it on fire. They failed. So they came back two-and-a-bit weeks later armed with a lot more petrol and more things to make it burn," he said.

Mr Tehan said there was no question burning the mosque was a serious arson "in the nature of a hate crime", but not terrorism.

"Mr Chaarani is entitled to be acquitted by you, perhaps even grudgingly, perhaps even unwillingly, if the prosecution cannot prove that this is something more than a terrible arson, and we say to you that they cannot prove that," he said.

John Kelly SC said his client Mohhamed simply wasn't there.

"It doesnt matter how many times you view the CCTV footage - backwards, forwards, 60 to 80 times, the submission doesn't change - that is not Mr Mohamed in the footage," he said.

Mohamed had appeared in a July 2015 photo with the IS flag as someone "a little on the immature side" attracted to the "superficial glamour of the flag" but Mr Kelly urged jurors to consider whether it had inspired the prosecution allegations.

Felicity Gerry QC, representing Moukhaiber, said the Imam Ali mosque was "no stranger to sabotage" and suggested there were "a dozen or so" other potential suspects including some with "large builds, shaven heads and beards" like her client, who would look similar on CCTV.

"The issues are, why was that Islamic centre gutted, and can the prosecution prove that (Moukhaiber) was the third man or not?"

Australian Associated Press