Under the system, PHOs and their general practices are paid according to the number of people enrolled - not the number of times a provider sees patients.
A dispute between Gill and Auckland DHB, regarding the issue of such payments, reached the High Court in 2010.
It focused on about 300 to 400 patients of her 2000-strong roll, and whether they were entitled to funding.
New Zealand Doctor reported that in November 2008, ministry officials and police raided Gill's Emily Place practice as part of an investigation.
It was suspected the doctor was incorrectly enrolling backpackers and patients attending casually for travel vaccinations and so receiving capitation funding.
Gill unsuccessfully appealed a High Court judicial review decision that upheld the ministry's right to search her practice and seize almost 40,000 patient records, the publication reported.
The 58-year-old GP was late for her court appearance yesterday morning and NZME. News Service understands a warrant for her arrest was cancelled when she turned up.
Gill did not return calls yesterday after numerous attempts to contact her.
According to property records, the doctor of 30 years and former high-school teacher owns a unit beside her clinic in town.
She is also registered as the co-owner of a bach on Waiheke Island and a home backing on to Cornwall Park, both of which are valued at more than $1m.
In 2003, Gill lost an Employment Relations Authority battle with a former receptionist and office manager over a spat about petty cash.
She had to pay $14,000 for the unjustified dismissal which the authority called "abrupt and harsh".
At the time Gill told the Herald she could not pay up as she was a single parent of four children dependent on family support to supplement modest earnings from her sole practice.
She will next appear before the court in two weeks.
Doctor's alleged fraud:
• Doctor is accused of deceiving the ministry for eight years
• 157 charges allege illegally-obtained payment of more than $435,600
• She was allegedly being paid for patients in Australia and the UK