Kumanjayi Little Baby, a name used in line with cultural tradition after her death, was reported missing from a home at a town camp on the outskirts of Alice Springs on April 25.
The five-year-old's disappearance triggered a five-day land and air search until her body was found in scrubland on April 30.
Jefferson Lewis, 47, has been charged with her murder and other offences.
A candlelight vigil was held at Alice Springs' Anzac Oval while other memorials for Kumanjayi Little Baby were held across Australia on Thursday evening.
Those attending were asked to wear pink, the little girl's favourite colour.
The Alice Springs vigil was held at the request of the girl's family who asked that their "sorry time" be respected, mayor Asta Hill said.Â
"This vigil will provide a time and space for us to all come together to stand with Kumanjayi Little Baby's family to hold this grief collectively," she told AAP.
Alice Springs had already shown how it could unite in support of each other, with many townsfolk voluntarily joining the five-day search for the girl in the desert heat.
Well over 1000 people gathered on the lawns outside Parliament House in Darwin, with territory politicians from all parties joining the sombre crowd to set down candles and sit on the grass.
Organiser Shalayne Calma-Reid told AAP a show of respect was needed with a quiet vigil for the little girl.
"It's really upsetting. I'm a mother myself so I can only imagine what the family is going through."
A woman in pink, who only wanted her first name used, told AAP it was important for the community to come together to share the sorrow.
"To show we are united in wanting to address the issues and hopefully bring about some change for the positive," Fiona said.
Charles Gauci, the Catholic Bishop of Darwin and the NT, said vigils were about prayer and mutual support and the Alice gathering was backed by the Ministers Fraternal, made up of a number of church denominations.
"In the midst of something so horrible and tragic ... it's absolutely vital that people get together," he told AAP.
"It's about being there for each other, it's about sharing grief together.
"Sharing your grief is so healthy because you don't just stay caught up in your own little self, you are part of something larger, you are not alone."
The vigils come as police continue to track down and arrest people who took part in rioting and looting triggered by the arrest of Lewis, with 30 people already charged.
Northern Territory Child Protection Minister Robyn Cahill on Wednesday confirmed three child protection officers had been stood down pending an investigation into how Kumanjayi Little Baby's welfare case was handled.
It's been revealed there were six recent reports made by police, women's shelter staff and a relative about the girl's living conditions and her potential exposure to harm.
A broader independent investigation into the structure of the department was needed, the minister told reporters on Wednesday, with a restructure down the track.
"There are so many children who have had repeated notifications made where zero action is taken for a number of years and those children subsequently have ended up in the criminal justice system," Ms Cahill said.
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