An Australian inquiry into child sex abuse is looking into how Melbourne's Northside Christian College handled complaints against a teacher accused and convicted of sexually abusing his students.

The teacher, Kenneth Sandilands, 69, was jailed for two years in 2000 for 13 counts of indecent assault of eight victims, the Guardian reported.

The Royal Commission into Institutional Responses to Child Sexual Abuse, which has far reaching powers to call witnesses, was examining the abuses committed by Sandilands in the 1980s and early 1990s.

Margaret Furlong, who still teaches at the college, said three children complained that Sandilands was touching them.

One girl, Emma Fretton, said she wanted to be transferred to another class "because he did bad things" to her.

Now 34, she told the commission that Sandilands abused her for three years, "touching her, beating her with a wooden paddle and making her sign obscene stories which the teacher dictates to her."

Furlong said she reported the complaints to the then principal but there was no action. She said the victims as well as the teachers got no support from the administration and a "climate of fear" pervaded the school.

She said at the time she trusted "godly men" to do the right thing.

Pastor Dennis Smith, a senior Pentecostal pastor, was asked why he did not question a report about the abuse.

"I was again being guided by the educators, the principal, because they would know what is right and what is wrong," he said. His answers also reveal that it did not occur to him that the reported contact may be a sexual contact with a child.

Smith also told the commission he had no reason to suspect Sandilands was touching children inappropriately because it was not his job to check previous employments of teachers.

On 10 September 2014, Sandilands was jailed for 26 months on a further six counts of indecent assault at St Paul's Anglican primary school in Frankston, Victoria, where he had worked in the 1970s before he joined Northside.

The commission was sitting in Sydney on Wednesday.