Detective Inspector Hayden Mander confirmed police have received the results from a number of tests and examinations.
"Those results, combined with a number of discussions with various experts, lead us to the conclusion that another person or people were involved in Maggie's tragic death," he said.
"We have carried out a considerable number of inquiries over the past three weeks and the investigation is ongoing."
Maggie was born in New Zealand, but her mother is Malaysian and her father is British. He no longer lives here and she had no other relatives in the country.
However, Mander said that police were in constant contact with her grandparents who live in Malaysia and her aunt who lives in the United States.
It is understood that police have interviewed several neighbours but it is unclear whether the child's mother has been formally interviewed.
Evelyn Sen has been in the custody of the Auckland District Health Board since the death.
Maggie's grandfather, Clifford Sen, told the Herald on Sunday he had received a letter from an attorney instructing him and his wife Patricia Sen not to talk about Evelyn Sen's medical condition and mental state.
"[The doctor's] indication to me is that she's recovering more or less, maybe a bit slow but she is recovering," he said.
He confirmed the police disclosed the findings of the second autopsy to the family. He did not want to reveal those details.
On the morning police were called to the home where Maggie lay dead, Evelyn Sen had also suffered minor injuries.
"We do not know what those minor injuries are or how she got them," said Clifford Sen.
The grandparents are still struggling to cope with the news of her death. The child had spent about two and a half months visiting them with her mother in Malaysia before she died.
"They were fine here. Maggie was beautiful and had a lovely time with my wife and me," said Clifford Sen.
"She was really good, really smart. I'll tell you she was so polite, so intelligent, so inquisitive. There's a lot of credit to Evelyn for that, for bringing her up so well."
He added that he was impressed that Maggie knew all her prayers, could say her ABCs and count her 123s.
"She loved looking at pictures and being able to describe them. She was so outward, she loved to talk about dinosaurs and the universe and things like that at her young age."
Maggie's grandmother, Patricia Sen, tearfully said she was struggling to cope with the death.
"She was a wonderful child. She really was an angel. As small as she was, she used to teach me. I'm not good at phone buttons, computer buttons but she would say 'come on grandma, you can do it.' Then when I'd done it she'd say 'good job grandma, awesome'."
Maggie is the sixth child under the age of 5 to be killed by another person in New Zealand this year.
Moko Sayviah Rangitoheriri, 3, died on August 10 after being admitted to Taupo Hospital with critical injuries.
Two people, a 26-year-old woman and a 43-year-old man, have been charged with assault on a child.
In July, 15-month-old Christchurch boy Ihaka Stokes died after being taken to hospital with fractured bones.
A 22-year-old man has been charged with his murder.
In June, a 6-month-old Kapiti girl died in Wellington Hospital from severe head injuries.
The baby's name has been suppressed and a 31-year-old man has been charged with assault.
In the same month, Esme Claire Kinraid died in Hawera. Her father was charged with manslaughter.
Leon Michael leFleming Jayet-Cole, 5, died in hospital after suffering serious injuries at his Christchurch home.
His stepfather has pleaded not guilty to his murder. His mother has been charged with failing to get her son medical treatment.
