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Sally Roberts, 37, has made headlines in Britain since she disappeared with son Neon a fortnight ago in the midst of a legal stoush over whether he should undergo radiation treatment following surgery to remove a brain tumour.
It sparked a nationwide search until police found them five days later.
Mrs Roberts, formerly of Auckland, fears radiotherapy could harm her son, but doctors say Neon will die within three months without treatment.
High Court Justice Sir David Bodey has now ruled Neon must have an operation to remove a 1.5sq cm tumour, the Daily Telegraph reported.
He said he sympathised with Mrs Roberts, but agreed with doctors that treatment was needed "extremely urgently".
Justice Bodey said all operations carried risks, and Neon's was no exception.
"But taking this on balance, against the expected gains to Neon in the unhappy position he now finds himself in, I am quite satisfied that surgery is in his best interests, and I shall make a decision accordingly so it can go ahead.
"We don't have the luxury of time ... and in the circumstances, the surgery must be done as soon as possible."
A recent MRI scan revealed Neon had a tumour in the same place his previous tumour had been removed from.
Doctors said the high-risk growth needed to be removed before Neon underwent further chemotherapy and radiation therapy.
Medical staff at a hospital, which the Telegraph said could not be named for legal reasons, are now preparing for an operation.
Mrs Roberts and her estranged husband, Londoner Ben Roberts, will be at the hospital from tomorrow.
The court heard Mrs Roberts did not consent to the treatment because the medical evidence was flawed and a second opinion was needed.
She initially agreed to surgery, but after thinking about it "long and hard", she decided against it.
"She is not persuaded of the need, and in particular she is not persuaded by the urgency," her lawyer said.
Mr Roberts, who was not in court, supported the team of experts calling for surgery.
The Telegraph reported Mrs Roberts has dismissed her legal team and appointed well known British human rights lawyer Imran Khan.
In a television interview last week, Mrs Roberts agreed running away with her son was "an act of desperation".
"I was on a conveyor belt and I had no choice. They said treatment must start. I thought if I was going to take him to the hospital they would never let us go home."
Mrs Roberts said she did not necessarily want to treat Neon with alternative medicines, but she wanted to explore options other than radiotherapy.
She said other medical professionals had contacted her in support of her position that other treatments were available.
"I feel we can still save his life. I'm incredibly confident. That's exactly why I don't just want to race into radiotherapy."
The surgery is expected to go ahead this week.