Ms Spencer thought her battle had come to an end when the Court of Appeal ruled last year that excluding payments to carers of disabled family members was discriminatory and in breach of their human rights.
She is now seeking a judicial review of the ministry's decision.
Her case was also singled out in Budget day legislation, passed under urgency in a single day, which prevents carers from seeking a judicial review in the future.
Her lawyer, Jim Farmer QC, told the court the ministry pays professional caregivers on average of $52,000 per year.
"But because he lives at home with his mother - who can be assumed does far more than a professional caregiver - the state pays nothing."
He said the ministry's position was contradictory because they do pay 272 family members to look after their disabled loved ones.
Mr Farmer said that figure made up 1.4 per cent of the 19,591 cases, and the ministry justified it through "cultural" reasons and for families living in rural areas.
He said the ministry relied on a "social contract" which states that the Government does not pay families to look after their own.
But Mr Farmer said the High Court had already found that the contract cannot apply to disabled adult children.
"If caregivers do hand over their adult children to the State, the State does pay probably more to the professional caregiver."
He said while the ministry estimated the costs of paying family caregivers was between $17 million and $593m, evidence from an economist suggests the cost to be between $32m and $64m.
Mr Farmer went through the history of Ms Spencer's case which included her approach to Helen Clark when she was prime minister. She had also written to the Governor-General.
He also read from correspondence between two Ministry of Health employees who discussed the case in which one described a previous legal hearing as a "great little outing".
The ministry employee went on to say Ms Spencer was "dragging poor Paul around like a teddy bear and telling the [Human Rights] Commission that she was a martyr."
Mr Farmer said the email was "indicative of attitudes" and explained why there was so much emotion in the case.
Human Rights Commission Andrew Butler told the court that Ms Spencer was not alone and there were others in her position with complaints before the Commission.
He said the new Public Health and Disability Act had "deep flaws". Parliamentarians were not shown legal advice and it was passed under urgency before going before a Select Committee.
The Court is yet to hear from Crown lawyers on behalf of the Ministry of Health.
The hearing - before Chief High Court Justice Helen Winkelmann - has been set down for three days.
