"It's nothing to worry about, it's simply reflecting the tighter operating environment where councils have deliberately been trying to keep the rates down ... and that potentially exposed us to slightly more deficit situations," he said.
Until 2008, councils had successive operating surpluses. Since that year, when the pinch of the recession was felt, there had been successive and growing deficits.
Mr Yule said councils that had heavily invested in infrastructure projects did not get the return they expected between 2008 and 2012 because of the financial crisis so their operating deficits had widened.
Hamilton City Council and Tauranga City Council had the largest budget deficits. Mr Yule said the two regions were responding to massive population growth.
Local Government Minister Chris Tremain said Government expected councils to achieve a surplus "unless there is a good reason not to".