Louis Francesco Rapisarda, 33, of Mitchelton, did not appear in Brisbane Magistrates Court on Friday for the first mention of charges of creating a public nuisance and disturbing a place of worship.
Police allege Rapisarda went to the Masjid Taqwa mosque at Bald Hills on May 10 and made verbal threats, telling worshippers he had an assault rifle in his vehicle outside.
He's accused of entering the mosque shortly before 11am and making the threat before he was chased off the grounds by members of the congregation.
No one was physically injured.
Rapisarda, a care support worker, did not enter a plea and was ordered not to attend the mosque or Mitchelton Presbyterian church.
His matter was adjourned until June 19 for mention.Â
Muslim leaders said the case was part of a growing wave of intimidation, abuse and violence targeting mosques and Islamic institutions.
The Australian Federation of Islamic Councils said the incident was "frightening" for worshippers and formed part of a "disturbing national pattern of threats, intimidation and violence" against Muslim communities.
AFIC president Rateb Jneid said the incident should not be dismissed as random, warning anti-Muslim hatred was shifting from online abuse into "physical threats, arson, intimidation and alleged acts of planned violence".
The Australian National Imams Council (ANIC) called the alleged threats a "grave violation" of the safety and sanctity of a place of worship.
It warned of the "increasing normalisation of anti-Muslim sentiment, threats, intimidation and acts of hatred" towards Australian Muslims and their mosques.
The Masjid Taqwa mosque was targeted in December when vandals sprayed a swastika and anti-Muslim graffiti on an exterior wall.
Local Labor MP Bisma Asif said a place of worship should be "a place of peace" and no one, regardless of faith, should fear for their safety when they gather to pray.
She said the rise in racism, Islamophobia and anti-Semitism had been fuelled by politicians using racial division to win votes and by those "too weak to call it out".
Both AFIC and ANIC welcomed the prompt police response and the laying of charges, saying they expected the alleged offending to be treated with the seriousness of a hate crime.
Police said all threats against cultural and religious communities were treated with the utmost seriousness and urged anyone who feels threatened or fearful to contact authorities.
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