“Alarming signs” that Ellie Butler was not safe with her parents should have raised red flags and prevented her return to the custody of the father who eventually murdered her, a children's charity has said.

The NSPCC said a family court judge's decision to allow the six-year-old to return to her "appalling" parents Ben Butler and Ellie Gray was the "pivotal moment" that led to her death and "possibly emboldened" her father's reign of violence.

Butler, 36, inflicted horrific head injuries on little Ellie while left home alone to look after her and her younger sibling in October 2013.

He was jailed for life today after being found guilty of murder and child cruelty following a trial at the Old Bailey. Jennie Gray, his partner and Ellie's mum, was found guilty of child cruelty and was jailed for 42 weeks.

Related: Family court judge 'handed all the power' to killer dad Ben Butler, finds serious case review into daughter Ellie's murder

Related: Ben Butler jailed for minimum of 23 years for murder of daughter Ellie

Butler was convicted of causing grievous bodily harm by shaking Ellie when she was just a few weeks old in 2007.

But he successfully appealed against the conviction and in 2010 won back custody of the little girl.

Less than a year after Ellie was placed back in her father's care, following a catalogue of violent abuse including a broken shoulder that went untreated for a month, he murdered her.

In a statement issued after the guilty verdicts today, a NSPCC spokesman said:“There will naturally be many serious questions about why and how this appalling couple were granted custody of their children, despite the alarming signs that should have raised red flags, but it’s worryingly clear the child’s voice was lost when it should have been the focus of attention.

“While this case is extreme the NSPCC has revealed today in its How Safe report the highest number of cruelty cases against children in England for a decade.

“The levels of violence in this case of child abuse may be exceptional but are by no means unique.”

Christine Davies, chair of Sutton Safeguarding Children Board, which today published a serious case review into Ellie's contact with authorities before her death, said the family court's decision had handed “all the power” to Butler.

She added: "The serious case review concluded that the family court’s decision to exonerate Ben Butler of harming Ellie in 2007, combined with its subsequent order for agencies to be sent a letter to that effect, had a very significant impact on how agencies could protect his children from that point in time onwards.

"Ben Butler’s exoneration and the judge’s statement about him being a victim of a miscarriage of justice had the effect of handing all the power to the parents. This coupled with the assessment made by services for children to support Ellie and her sibling to be cared for by their parents were critical factors."

An NSPCC spokesman said:“The serious case review makes it plain the pivotal moment in this dreadful case came when Butler’s earlier conviction for causing Ellie life threatening injuries was quashed by the High Court.

“There is no doubt this put social workers on the back foot and possibly emboldened him to continue with his violent campaign against a helpless child.

"Butler confronted social workers with aggression and black-hearted deception and even now appears unwilling to accept responsibility for his terrible actions."