An arsonist is believed to be behind a fire which seriously damaged the only mosque in Toowoomba, on Queensland's Darling Downs.

A glass panel at the entrance of the mosque was smashed before it was set alight about 2:00am Friday.

Firefighters managed to put out the blaze, but not before the building was significantly damaged.

There are no suspects at the moment, but it was the second attack on the mosque this year.

Acting Superintendent Ben Marcus said arson had not been ruled out.

"It's an obvious line of inquiry for us," he said.

In January, a man tried to light a fire in a plastic bin and then deliberately left a gas stove on in a building adjoining the mosque, but it failed to ignite.

Security and police patrols have been stepped up over the last six months and worshippers have been warned to be careful in the area.

The blaze is believed to have started in the office and quickly spread throughout the building.

Toowoomba Mayor Paul Antonio said the region aims to promote peace and harmony.

"To see the events of the last 24 hours here in this beautiful garden city is something that disturbs us all."

Toowoomba's Muslim community took their prayers to a park today, because their mosque is now a crime scene.

Under police protection, the congregation was asked to be patient, rather than angry.

'A silly, stupid thing'

Islamic Council of Queensland president Ismail Cajee condemned the attack.

"Whoever has done it is totally illiterate and absolutely uneducated," he said.

It is the second attack on the mosque this year, with a man trying to light a fire in January. ( Facebook - file photo )

"If only they knew and understood that the religion of Islam has been there for the past 1,400 years like the other religions, like Christianity, Hinduism, like Judaism.

"It is because of their illiteracy that they would do such a silly, stupid thing."

Toowoomba Islamic Council president Professor Shahjahan Khan said the damage was devastating, with parts of the brick building burnt to the ground.

"It's huge damage to this property," he said.

Professor Khan said the city's wider community had been accepting since the mosque opened 12 months ago.

"This is an act of one or two people and is no reflection of the Toowoomba people I know," he said.

"The group of people who've done these kinds of things have not done anything good for themselves or the city."

He said prayers would now be held in an adjoining building.

Professor Khan said a open day and world food festival planned for this Sunday would still go ahead.