New Zealand's oldest missing person case is set to close more than half a century after police began investigating the disappearance.

Morrinsville toddler Betty Wharton was last seen in 1964 and despite more than 52 years of investigations, the case was never solved.

Police are now preparing to officially close the case and refer Betty's disappearance to the Coroner, Fairfax reported.

Betty was the daughter of farm workers Charlie and Marion Wharton.

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For many years they were considered suspects in the little girls' disappearance.

The couple spent time in jail after the death of Betty's older sister after they were convicted of failing to provide the necessaries of life.

They were being monitored by authorities, but as they moved around a lot for work the couple fell through the cracks.

When child welfare workers eventually located the Whartons, Betty was no longer with them.

The couple told police that Betty was in the care of her grandfather, but later changed their story to say she had been informally adopted by Te Awamutu woman named Martha.

Both Marion and Charlie Wharton have passed away and the mystery of Betty's fate likely died with them.

Fairfax reported today that Betty's case is the oldest among the 143,000 active cases under police investigation and the file would soon be referred to the Coroner.

The Coroner can then hold an inquest into Betty's disappearance and officially declare her dead if there is no evidence to support any other outcome.

Fairfax also revealed that there are currently 11,500 active police cases in the Counties Manukau district, 8006 in Auckland City and 6888 in Waitemata.