He is not the father of the boy.
"Today's arrest is the result of countless hours of work by a team of investigators who have investigated this child's tragic death," said Detective Senior Sergeant Geoff Baber.
He could not comment further as the matter is now before the courts.
Little Malcolm was rushed to Starship by ambulance with critical injuries on Sunday June 23.
He died six days later, sparking a homicide investigation involving upward of 20 police.
Police were alerted to Malcolm's injuries by hospital staff who believed he had been deliberately harmed.
Malcolm has five older siblings who have all been removed from his mother's care by Oranga Tamariki.
All five children are currently in the care of others.
Malcolm's mother has refused to speak to the Herald.
"I have had legal advice and I will not be speaking to the media," Savanna Bell said when approached for comment.
When her son was six months old she posted about him on Facebook.
"Watching you grow makes me so happy," she wrote.
"Your first word was mama I was so happy when I heard you say mama.
"You have an awesome personality my son Malcolm your (sic) growing every single day and night ... I love you always my son."
A month later she updated her family and friends again.
"I'm so proud to b your mama your (sic) learning how to crawl," she wrote.
"Son I learn new stuff from you every day my baby."
After Malcolm died and his name was released publicly, his mother deactivated her social media profile.
Her sister posted a photograph of the baby in hospital soon before he died.
"Sitting here with you watching you holding on is so heartbreaking," she wrote.
"My heart breaks even more with every breath you take knowing it could be your last.
"We love you Mr and always will."
Malcolm's father was not in a relationship with Bell when he died.
He lives with his new partner and other children out of Auckland.
After Malcolm died the partner posted online that "losing your own kid" was "the most heartbreaking" feeling.
Last month Children's Commissioner Judge Andrew Becroft announced a review into Oranga Tamariki's child uplift policies relating to care and protection issues for Māori babies.
It follows controversy over the attempted uplift last month of a young Māori mother's baby from Hawke's Bay Hospital.
The "thematic review" will look specifically at policies around Māori infants aged 0-3 months.
Judge Becroft said while the review would initially focus on the 0-3 months age group, he could not rule out extending the review to older children.
He said his office had a statutory mandate to investigate.
"If we didn't do it we would be asleep at the wheel," he said.
The same day Judge Becroft announced his review, Minister for Children Tracey Martin announced an internal inquiry by Oranga Tamariki into its processes, specifically around the Hasting family's case.