Margaret Furlong began working in the primary school section of the college in 1987 when she was 23.
She told the commission she repeatedly raised concerns with the principal about students who said they had been touched by Sandilands, who was later jailed for indecent assault.
Mrs Furlong said a culture of fear, bullying and harassment may have contributed to preventing the exposure of child sexual abuse.
"We were terrified and frightened to say anything about anything that was going on in the college for fear of reprisal from Pastor Denis Smith," she said, referring to the school's former senior pastor.
|Margaret Furlong, teacher at Northside Christian College|
"From the very first day that I was employed at the college, we were told that the college was a ministry arm of the church, and we were under Pastor Smith and under God," she said.
Ms Furlong said principal Neil Rookes, who has since died, appeared to do nothing and she regretted not going to police with her concerns about one child, Emma Fretton.
"No-one ever spoke to me or I was never asked to write anything down," she said.
"I didn't know what to do. I wish now that I had gone to the police.
"I wish I had contacted Emma's mother. I wish I had done something else.
"But I was an intimidated, inexperienced and gullible person at the time, and what I did was to try to the best of my ability to protect Emma."
Pastor Smith told the commission he had no reason to suspect Sandilands was touching children inappropriately.
"I was not involved in vetting him," Pastor Smith said.
"Everything I received was positive and on the basis of that I agreed to the appointment of him."
On September 10, 2014, Sandilands was convicted of six counts of indecently assaulting a girl and one count of indecently assaulting a male under 16 at St Paul’s Anglican Primary School in Frankston, Victoria.
The offences happened a decade before he began work at the Northside Christian College.
Pastor Smith was asked why he did not question a report that a girl was touched on her lower stomach.
"I was again being guided by the educators, the principal, because they would know what is right and what is wrong," he said. Wow! Being kept in the dark is one thing, but deliberately turning out the lights is something completely different. A senior pastor who allows others to decide what's right and what's wrong is a little hard to believe.
He was asked: "Did it not occur to you at the time that that sort of contact may well have been sexual contact with a child?"
"No, it did not," he said. Good grief!
Mrs Furlong revealed she was abused as a child and entered the job "with no belief in the legal system to deal fairly with the victims of child abuse".
"I put my trust in people I thought would do the right thing. People that I classed as godly men," she said.
"These men did not do the right thing, and they did not support myself and other staff members in dealing with these allegations or anything else."
Mrs Furlong still teaches at Northside Christian College and said it was a very different place today.
|Northside Christian College, Melbourne|
The former deputy principal of the college broke down while giving evidence at the inquiry.
Simon Murray told today's hearing he had been devastated by the evidence so far.
"I've been deeply impacted as I've learned for the first time why some of the children at a school I taught at suffered ... and I want to say to you all that I've been overwhelmed as I read and heard what you went through," he said.
Mr Murray sobbed and added that he admired victims' "courage and resilience".
"I am extremely upset that I didn't know at the time and I feel deeply for you ... and I hope that this process plays a part in continuing to build your lives," he said.
The hearings continue in Sydney until October 17.