Child protection advocates say legislation which has now passed the South Australian Parliament falls short of what is needed to protect the state's most vulnerable.

The Children and Young People (Safety) Bill was a response to royal commission recommendations, and will replace the state's current children's protection laws.

Social welfare and legal groups expressed many objections to the legislation, slowing its passage through Parliament.

They did not want to see guardianship responsibility transferred from the minister to the chief executive of the state's child protection department, and objected to replacing the words "best interest of the child" with "protecting children from harm".

Opposition Leader Steven Marshall said his party opposed the bill because of such objections.

"We are very concerned that the very strong community expectations for the sector have not been met with this current version of the bill," he said.

The Liberal Opposition and minor parties made many attempts to amend the bill before it finally passed with only a handful of the suggested changes succeeding.

Those included a clause about female genital mutilation and expanding what the Civil and Administrative Tribunal could review.

Council for the Care of Children executive Simon Schrapel said the legislation remained inadequate but the amendments had improved it.

"It remains far from a perfect bill and has a number of deficiencies but, nonetheless, we certainly applaud the work of the Legislative Council members to get some amendments through," he said.

"It has strengthened the bill, particularly in relation to ensuring a future government will need to commit more resources to family support.

"As the state with the lowest level of expenditure per child on family support and preservation in Australia, something had to be done to right this imbalance."

'Not about the parents', Rau says

SA's Attorney-General and Child Protection Reform Minister John Rau was scathing of the Opposition's efforts to thwart the changes.

"We're putting the children at the centre of this — it's not about primarily what parents want," he said.

"If parents get to the point where their parenting is so bad the state takes the child away, surely we've got to the point that it's about time we listened to the child."

Mr Rau said the changes would reset the area of child protection after a series of failings.

"It's not going to solve every problem overnight but it is going to mean that those very, very vulnerable children who are at serious risk of harm are going to be taken away in a timely fashion, before the harm is allowed to make them even more damaged than they might otherwise be," he said.

"They're going to be in a safe environment where they can have some stability."

Child Protection Minister Susan Close said departmental staff remained able to exercise sound professional judgment.

"For staff, the new bill enables greater ability to act proactively to protect children and young people at risk of further harm," she said.

"The bill respects the professional judgment of those who know the children, young people, families and carers, so those decisions are best informed and have the greatest opportunity to result in positive outcomes."

Critics said the legislation also lacked a focus on preventing children from ending up in care.

The SA Government said it would introduce an early intervention bill before the end of the year.