Council group manager support services Alan Adcock said this $12m figure was due to a series of "noisy" accounting adjustments, including interest rate swaps and assets vested to the council.
The council also decreased its net debt ($136m) and stayed below its $2150 per capita target, though it had borrowed internally to fund transportation and parks infrastructure.
"It's been a good year, though of course I would say that," said Mr Adcock.
"Council is back in the black. The [Long Term Plan] was about getting back to a balanced budget, which we've achieved."
The council met 74 per cent of its non-financial targets, with problem areas including an increase in refuse - tonnage increased 6.1 per cent but the target was a 2 per cent decrease. The council put this down to population growth and noted a 12.7 per cent increase in recycling tonnage.
Also in the fail column was resident satisfaction with the roading network, balanced by good performance across walking and cycling measures, in a year where people were satisfied with footpath conditions and the cycleway network expanded.
Eighty-two per cent of people felt safe in Whangarei, compared with 87 per cent last year. Council's target was 85 per cent. Most people who did not feel safe cited "a general sense of too much crime".
Two out of three of the council's economic growth indicators were also fails, with Whangarei's GDP growing slower than similar regional economies, and guest nights down 9 per cent year-on-year.
Mr Adcock said targets were measured on a pass/fail basis, so even where performance was relatively good, it could be a fail. Despite 56 per cent of residents using a library in the past year, this was a fail because the council aimed for 60 per cent.
In the case of economic growth, measures were not directly within the control of council.
"It's hard to get a measure that isolates the effect that council has had on something when you come up with these measures."