"[Last registration period] 97.3 per cent of dogs were registered.
"So there's about 2 per cent which we know about that aren't.
"That is 10,050 in total.
"[But] we also think there's about 5 per cent - which is an estimate of 500 dogs - that haven't come to our attention," said Mr Lincoln.
He said the council had a "zero tolerance" for such dogs.
"If a dog control officer encounters an unregistered dog, then in addition to any registration fee that may be due, the owner will receive a $300 infringement notice."
As well as this, if an unregistered dog is impounded, owners must pay $50 before they can retrieve it.
This is slightly more than a registered dog, which will cost an owner $40 for release.
If a dog is impounded a second time, an owner will have have to fork out $75 for its release. Any subsequent visits will cost them $125. Owners also have to pay a $7 sustenance fee for each day their dog is impounded.
Mr Lincoln said while pound fees were structured to deter reoffending, there were some dogs which were continually being picked up by animal control officers. "We do get serial offenders - the worst has been in the pound 14 times over a three year period."
The animal services team leader said an increase of 550 in the city's dog population reflected the larger number of complaints against dogs.
Figures showed a total of 3671 complaints were responded to by the dog control team in the 2011/2012 period, up from 3235 in the previous period.
Despite this, there had been a decrease in the number of reported dog attacks,down from 82 in 2010/2011 to 69 between 2011/20012.
When taking into account the increase in dog numbers, this is the lowest rate of attacks for a number of years, said Mr Lincoln.
Labrador retrievers were also revealed to be the breed of choice for Tauranga dog owners.
At 1484 in total, the popular dog makes up almost 15 per cent of the city's canine population, dwarfing the smooth haired fox terrier - which comes in a distant second with 621 registered members.