The figure is revealed in a financial report from finance and funding general manager Robert Mackway-Jones to tomorrow's board meeting in Queenstown.
Parts of the 2011-12 clinical programme were signed last week, meaning about half the "services to improve access" funds for high-needs patients can be used from the end of August, Mr Mackway-Jones said.
Another portion of the funds - specifically for health promotion - remain unused.
Contacted by the Otago Daily Times, SPHO chief executive Ian Macara said the three most important health programmes were signed last week - sexual health, cardiovascular risk and diabetes.
"The money is not lost because the volumes will just be used from now on, for the 10 months," he said.
It had never been SPHO's plan to have all programmes ready for the start of the 2011-12 financial year, and indicated funds for some programmes might not stretch to a whole year.
The 2011-12 plan was likely to be in place by the end of the calendar year.
It was crucial to consult clinicians to get programmes correctly targeted for the best use of funds.
The clinical plan is SPHO's first since forming last October and attracted some controversy because of proposals to fund procedures usually associated with district health boards, such as colonoscopy.
SPHO also proposed spending $250,000 helping adults with poor teeth.
Mr Macara said the oral health plan looked set to be changed by clinicians who sought funds for more emergency dental treatment over tooth extractions.
"Southern PHO development" appears as a separate agenda item for discussion at the meeting, in the public-excluded session, with commercial activities and negotiation cited as the reason for discussing it behind closed doors.
After a query by the Otago Daily Times, chief executive Brian Rousseau said he had re-examined the material, and decided part of it would be moved to the open session of the meeting.
