The CHFA, the "banker for DHBs", said 15 out of 21 boards were operating in deficit, two more than in June last year.
District health boards' deficits are expected to total $200 million in the 2009-10 financial year.
The increased deficit, up from $43 million in 2007-08, was driven by boards' inability to control increasing costs as revenue fell, the CHFA stated.
The seven DHBs were considered "at risk" because they needed remedial action to justify continued CHFA funding.
The at-risk DHBs are Tairawhiti (East Coast), Hawkes Bay, Whanganui, Capital and Coast, West Coast, Otago and Southland.
The situation had become apparent in the past 12 to 18 months and there was a marked variation in boards' performance over the past year.
Paying staff was the biggest single cost, representing more than one third of total costs to boards, CHFA chairman John Anderson said.
Staff costs were driven by multi-employee collective agreements, staff shortages leading to increased overtime costs and locum costs, and inflexible workforce arrangements.
Otago's deficit this year is expected to be $12 million and Southland's $9.9 million.
At its meeting today the Otago board will be told its advanced funding status for next year is unclear.
When boards are paid in arrears, it means they lose the ability to gain interest on advance funding.
Regional chief financial officer Robert Mackway-Jones, in his report to the meeting, also said the deficit support was likely to be lower than planned.
The board has to make a financial recovery plan to show how it can achieve financial sustainability and break even in the next three years.
How the board will fund long-overdue upgrading to some of its substandard facilities is also of increasing concern.
The health select committee was told by CHFA chief executive Graeme Bell the Crown's ability to increase operational spending was constrained by the growth of the economy and over the past few years board costs had exceeded that rate.
The sector also varied in how well financial discipline was applied at the local level, he said.
In many cases, boards were reliant on key people to focus on financial performance and that was something that could be looked at in any review.
