He will next appear in the High Court at Auckland in August.
Malcolm died on June 29, six days after he was rushed to hospital.
Up to 20 police were involved in the investigation into his death.
"The death of any child is an absolute tragedy and we are working hard to establish what has caused the child's injuries," Detective Senior Sergeant Geoff Baber said when the homicide investigation was launched.
Malcolm's mother has previously declined 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.
The Herald understands Malcolm's five older siblings had all been removed from his mother's care by Oranga Tamariki. They are all currently in the care of others.
During the first year of Malcolm's life his mother wrote the following 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."
After Malcolm died and his name was released publicly, his mother deactivated her social media profile.
