A mother is expected to be charged with the murder of her toddler who went missing from the NSW Hunter Valley 15 years ago.

Leonie Astra Hutchinson was 16 months old when she disappeared from her home in Scone in 2001.

A 2013 inquest heard Kate Hutchinson was involved in witchcraft. ( Supplied: NSW Police )

But she was not officially reported missing until January 2004.

Detectives arrested the toddler's mother, Kate Hutchinson, at her home in Evans Head on the state's far north coast this morning.

The 43-year-old is currently being questioned at Lismore Police Station and is expected to be charged with the child's murder.

An inquest in 2013 heard Ms Hutchinson was involved in witchcraft and told people her daughter was staying with friends.

The inquest also heard allegations Ms Hutchinson told a colleague that she killed her daughter and that her body may have been dumped in a well.

The house in Scone where Leonie Hutchinson was last seen. ( ABC News: Jackson Vernon )

A lead detective on the case told the hearing the property Ms Hutchinson once lived on had a deep well on its grounds, and the child may have been "secreted" there if she was dead.

The case has been the focus of three coronial inquests, the last of which in 2013 lead police to search a property in Scone.

An inquest in 2011 heard from two friends of Ms Hutchinson who said the mother had a bad experience on the drug LSD and would constantly talk about being scared of a "wolf-man".

The court heard from the friends that in the years before Leonie was born, Ms Hutchinson had talked about having a daughter and making a sacrifice to keep the "wolf-man" away.