Mr Lincoln said there was also an estimated 500 dogs in the city unknown to council.
There were 3671 dog complaints in 2011/2012 and the total number of dog complaints for this financial year was expected to reach 3800-3900 - the large majority relating to barking dogs.
Mr Lincoln said the increase in complaints correlated with the jump in dog numbers and "intensification" in the city.
"It means it is vitally important that we closely manage the city's dogs and their owners, including ensuring dogs are all registered, and owner/s are educated how to manage their dog's behaviour.
"There is a lot of responsibility on owners, not just to feed and water their dogs, provide shelter and exercise them, but they also need to ensure they don't roam, and when out walking with their dog they clip them onto a lead," he said.
Mr Lincoln said from July 1 to the end of May this year there were 76 reported attacks on people compared to 69 between 2011/2012 and on average two to three dog owners were prosecuted each year. "Prosecution does depend upon the seriousness of the incident, the history of the animal and its owner, but in general we only prosecute as a last resort," he said.
Mr Lincoln said since July 1 last year four prosecution cases were resolved, that included the owner of a dog who was fined $500 and ordered to pay $1500 after it attacked a bus driver who went to the aid of some children in August last year. In each case the offending dog was destroyed.
Mr Lincoln said there are two active prosecutions before the courts - one related to a dangerous dog being found in public unmuzzled, and the other was a dog accused of killing a cat. The large majority of dog problems related to unregistered or roaming dogs, he said.
There were 801 dogs rounded up this financial year compared to 998 in 2011/2012, of which 461 or more than 50 per cent were unregistered - 81 per cent were returned to their owners, and the rest were deemed unsuitable to be adopted. He said any dog over the age of three months must be registered, and unregistered dogs attract an infringement fee of $300 plus the registration fee.