The head of a pentecostal Christian college in Victoria failed to protect students even though there was abundant evidence they were being sexually abused, a royal commission has found.

In a report released on Friday, the Royal Commission into Institutional Responses to Child Sexual Abuse is heavily critical of how Northside Christian College and its affiliated pentecostal church in Victoria handled complaints against pedophile Kenneth Sandilands, who was jailed in 2001.

In October last year, the commission examined how a number of Australian Christian Churches (former Assemblies of God) institutions in Australia responded to abuse allegations.

Northside Christian College at Bundoora in Melbourne's northeast, and the Sunshine Coast Church in Queensland, as well as Hillsong in NSW, were among those investigated.

The commission heard evidence from Emma Fretton, a former student at Northside, who was abused by Sandilands for four years from the time she was six.

From 1987 to 1993, other children came forward to staff at the college to say Sandilands had sexually abused them.

In 1987 the then chair of the church board, Pastor Denis Smith, and college principal Neil Rookes, set behavioural guidelines for Sandilands but he didn't adhere to them, and Pastor Smith was made aware of this.

"The commissioners are satisfied that Pastor Smith had sufficient knowledge that Mr Sandilands posed an unacceptable risk to children at the college from the late 1980s and failed to act to ensure the protection of the children."

The commission was also critical of the actions of Ian Lehmann, a senior pastor at the Sunshine Coast Church in 2004, when Jonathan Baldwin was hired as a youth pastor.

Within a few months, Baldwin, who later married Dr Lehmann's daughter, began sexually abusing a 13-year-old boy, "ALA". For two years, the abuse continued and escalated.

The commissioners expressed the view that "Dr Lehmann failed to recognise the indicators of risk of child sexual abuse ... despite personally observing some indicative behaviour and receiving reports of concerns from members of the pastoral team and directors of the board of the Sunshine Coast Church".

Baldwin did not hold a credential from Australian Christian Churches (ACA) - that this could happen was identified as a weakness in the necessary controls to keep children safe.

In a statement on Friday the ACA said it had actively addressed many of the points that emerged at the royal commission hearing and their child protection policy adopted in 2015 was binding on all credential holders and constituent churches.