A man accused of murdering a toddler left an answer phone message saying sorry just moments after he inflicted her fatal head injuries, a court has heard.

Aaron Archer could be heard saying "I'm sorry ... Ariah, Ariah" in the message played to the jury at the High Court in Auckland on Thursday. 

The Crown claims Archer caused the 2-year-old's fatal injuries while her mother was out shopping for groceries on August 22, 2018.

Archer denies her murder, instead claiming she was injured when she accidentally hit a wall as he lost his grip while spinning her around as they played together. 

On Thursday, the court heard Archer phoned Ariah's mother soon after Ariah was fatally injured.

She did not answer but the emotional message was recorded on her phone.

The recording appears to begin with the sound of Archer vomiting, before he says "no, no, no, Ariah."

He then calls out the mother's name before saying: "Ariah, come on, it's ok. Ariah, no, no. Ariah, no."

Later he can be heard saying: "I'm sorry... Ariah, Ariah, Ariah ... no."

Giving evidence, Ariah's mother, who has name suppression, said she phoned Archer back after seeing the missed call on her phone, and Archer told her Ariah wasn't breathing.

She said Archer put the phone down but did not hang up and she could hear him telling Ariah to breathe.

"I was just screaming: 'Call the ambulance, call the neighbours'."

The mother said she almost crashed her car in the rush to get home.

Once inside the house, the mother said she screamed for her daughter and eventually found the toddler on her bed, covered in her dressing gown.

"She was just very pale and very limp."

She told the court she put her daughter down on the sofa and went to get help.

Her neighbour Steve Taua performed CPR, while Taua's wife Helen called an ambulance.

Later, the mother talked of waiting outside the unit with her mother and Archer as firefighters and ambulance staff tried to save her daughter.

"I heard [Archer] say to my Mum that he was chucking her up in the air and she hit her head."

"I just remember the family tried to keep Aaron away from me because it was stressing me out."

A doctor later came out of the house to tell her Ariah had died.

"I knew she'd passed away when they lowered the curtains down," she said.

The mother told the court how she and Archer had been in a relationship for about six months and had been living in the unit in Mangawhai together for about five months.

Crown prosecutor Brian Dickey asked her how Archer got on with Ariah.

"There were no problems at all, just ... I would ... I wouldn't like... have someone in the house that would endanger safety."

She described her daughter as her "miracle child", having been born prematurely with a twin brother who died at birth.

Dickey also asked about bruises Ariah had before she was left alone in the house with Archer.

The mother said Ariah had a bruise on her temple and one on her eye, adding: "She was starting to walk so she was falling over a lot."

Under cross-examination from Archer's lawyer, Ron Mansfield, the mother confirmed Archer would help her with Ariah and Archer would play with her.

"I would never have left her with anyone I didn't trust completely."

She agreed with Mansfield that she and Archer would occasionally hold Ariah by the hands or wrists and spin her around.

The mother agreed that after the incident, Archer looked a wreck, was in shock and upset.

Earlier, jurors heard from pathologist, Rexson Tse, who performed the autopsy on Ariah.

He said it was "very unlikely" her injuries happened by accident.

He found 24 bruises on the toddler's body, with most on her head and face.

The number, pattern and size of the bruises were not normally found on children as a result of everyday bumps and thumps, the court heard.

"These are classical of abusive head trauma," Tse said.

"Therefore, it is very very unlikely that they're accidental."

Crown prosecutor Brian Dickey asked if the injuries to Ariah could be explained by her accidentally banging her head against a wall.

"That could explain one or two bruises but not 20," Tse said.

Under cross-examination from Archer's lawyer, Ron Mansfield, Dr Tse resisted Mansfield's suggestion that many of the bruises could be explained by the child falling over or accidentally bumping her head on a wall or her cot.

He said research analysing 1000 children found the majority of accidental bruises were found on the child's forehead or chin.

In only one case did researchers find a bruise on the side of the head.

Mansfield asked if some of the bruises could be explained by emergency staff trying to perform CPR.

Dr Tse said that kind of bruising would be confined to the chin and mouth area.

The trial continues.