The schoolgirls were attending the career expo at the Perth Convention and Exhibition Centre (PCEC) last week, just days after the suicide bombing in Manchester that left 22 dead and dozens injured.
Some people complained that the school children's hijabs were "making them feel uncomfortable after what happened in Manchester" and asked staff to have them removed from the venue, WA Today reported.
The PCEC confirmed the centre was contacted about an alleged incident involving discrimination against patrons on May 26 but denied that their staff were involved.
The incident came just over a week after Salman Abedi killed 22 people in the suicide bomb attack in Manchester at an Ariana Grande concert.
A mother of one of the students was quoted as saying that her 16-year-old daughter was at the Careers Expo at the Convention Centre last week when she and her school friends were told by their teacher that they had to pack up their lunch and leave.
"I'm not angry, I'm just sad," the mother of the student was quoted as saying by the daily.
"I feel particularly sad that my daughter went on an excursion and didn't enjoy it. I see this as an opportunity to raise awareness and get a deeper understanding of how young Muslims in Australia feel," she said.
Islamophobia Register Australia President, Mariam Veiszadeh, said she was "very disappointed to hear about the incident."
"Time and time again, we come across examples of ignorant prejudice in which every day people conflate the faith of 1.6 plus billion Muslims worldwide with that of the murderous acts of a group who hold themselves out to be Muslims," Mariam Veiszadeh said.
"Women often bear the brunt of Islamophobia and a rather alarming number of incidents take place in the presence of children," she said.
A spokesperson for PCEC said the centre did not condone discrimination of any kind.
"All staff are aware of this as a condition of employment," he was quoted as saying.
"After an internal investigation, the centre does not believe any of the PCEC's staff were involved in such an event," the spokesperson said.