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Ms McSkimming said microchipped pets that were not registered on the New Zealand Companion Animal Register were being brought to the SPCA's North Dunedin shelter.
A cat owner, who was reunited with his missing microchipped cat on Monday, had not logged it on the register, which had delayed the pet's return home, she said.
After an animal was microchipped, vets could register pets on databases that the SPCA could not access, whereas the national register was accessible to anyone, she said.
''It would be good if there was one database.''
When dogs were microchipped, their details were not recorded on any databases until they was registered with the relevant city council.
Once dogs were registered at the council, their details were placed on a national council database, which was not available to vets or the SPCA.
The council database was an enforcement, rather than ''repatriation'', tool.
If a dog owner placed their pet's details on the national register, the SPCA could then contact the owner directly without involving the council, Ms McSkimming said.
New Zealand Companion Animal Register manager Nygllhuw Morris said the resister started about seven years ago and was used by 97% of vets.
The register of 280,000 ''companion animals'' - which includes microchipped cats, dogs, goats, ferrets and horses - was set up ''purely to get animals home''.
After the Canterbury earthquakes in 2010 and 2011, register staff had reunited most non-chipped pets with their owners within one or two weeks, while 85% of microchipped pets were returned to owners within 12 hours.
''It's a very effective tool, but it's only effective if you microchip and register. If you just stick the microchip in there and don't record it anywhere, it is a complete waste of time,'' Mr Morris said.
Animals can be registered for $15. Details at www.animalregister.co.nz