Western Australia Police say they are hunting three people after a car was set alight and offensive graffiti was sprayed on the wall of an Islamic college in Western Australia's capital on Tuesday night.

Hundreds of people were praying at the college's mosque when a Toyota Prado was doused in petrol and set on fire, according to investigators. Other cars in the vicinity were also damaged.

The offenders also sprayed anti-Islamic graffiti on the walls.

Witnesses say they saw three people running from the college.

"We were praying peacefully when we heard the noise," says one mosque attendee.

"We saw the smoke. It was scary."

But after some time, when prayer-goers saw that emergency services and police were there, they went back into the mosque.

Thornlie Mosque and Australian Islamic College leader Yahya Adel Ibrahim described the incident as a hate crime.

Local father Aaron lays what he calls a symbol of love outside the targetted Australian Islamic College in Thornlie pic.twitter.com/PFbbTRRinC — Ryan Emery SBS (@ryanremery) June 29, 2016

"This, undoubtedly is a criminal act of hate," he wrote on his Instagram account.

But he adds his community won't let the incident affect them.

"Despite what just transpired, everyone stayed to finish their prayers refusing to give into the terror that had just occurred."

The #Perth community was visited this evening by hate. A suspected petrol bomb was placed in a… https://t.co/O1tgVw24MB — Yahya Adel Ibrahim (@yahya_ibrahim) June 28, 2016

Prime Minister Malcolm Turnbull stated on Wednesday he "deplored" the incident.

"[Australia is] founded on a fundamental, a foundation of mutual respect," he told media.

"I cannot condemn strongly enough any attacks of that kind."

Foreign Minister Julie Bishop told a media conference in Perth that the Australian Federal Police would investigate the motives.

But she sidestepped questions about whether the attack could be linked to recent government rhetoric around border security and asylum seekers in the lead up to the federal election.

"The Australian government condemns any form of violence and we will work exceedingly hard to ensure Australians are kept safe," Ms Bishop told reporters.

The local MP whose electorate covers Thornlie, Chris Tallentire, told 6PR radio the attack was "sad".

"Thank goodness no one was hurt but really this has to be described as an act of urban terror," he said.

Australian Islamic College executive principal Abdullah Khan told ABC News while he was shocked by the attack the remainder of the week would be business as usual.

But he adds he would like greater police presence in the area during the final days of Ramadan.

No one was injured in the attack.

-With AAP