Churches are still failing to take children's claims of abuse seriously, a new report from Victoria's Commission for Children and Young People (CCYP) has found.

The latest annual report from the CCYP also showed that some major institutions were struggling to meet their obligations, a year after mandatory abuse reporting laws came into effect.

The report, which was tabled in State Parliament, said more than 1,300 allegations of child abuse were made in schools, out-of-home care, churches and similar institutions across Victoria.

The allegations include both physical and sexual abuse, and the CCYP's principal commissioner, Liana Buchanan, said the number of reported cases was significant.

"The issues we saw through the royal commission are not historical and remain a concern today," she said.

More than half of all cases occurred in out-of-home care (366) and schools (289).

Those figures dwarf the 22 notifications of abuse in the church, though those sectors' vigilance and readiness to report are considered a factor in their larger numbers.

Churches also only began reporting cases of abuse in January.

The report found physical violence was the most common form of abuse in every sector except for religious organisations, where sexual abuse was predominant.

"It's the first time we've had visibility of the scale of the complaints," Ms Buchanan said.

"We have seen massive variability and examples of very poor practice, even among some well-established organisations.

"We've seen some poor practice, including by sophisticated organisations that I would have thought should know better.

"We still see cases of children not being believed, of children not being asked what had happened to them, and a tendency for organisations to pre-judge a complaint in favour of trusted adults.

"Despite all the evidence that organisations have too often mishandled allegations of abuse, I still see many of the themes from that royal commission in investigations today."