Both islands are pest-free and Moturua is home to endangered birds such as the tieke (saddleback).
On Monday DoC staff, working with private landowners on the island, finally managed to catch the cat in a cage trap using tinned tuna as bait.
Senior biodiversity ranger Adrian Walker said the cat's owners did the right thing by calling DoC as soon as they knew their pet was missing.
However, he urged boaties to act responsibly and not take their pets near islands where wildlife could be put at risk.
Mr Walker said volunteers and hapu had put a lot of effort into Project Island Song, which aims to restore the islands' wildlife, but it could be undone by people re-introducing pests or predators.
The "completely preventable" search for the cat had taken up staff time and cost the taxpayer an estimated $5000.
The cat had been returned to its owners, who were remorseful and agreed not to take their pet on board again. There was no law allowing DoC to impose a fine, Mr Walker said.
The cat was in good condition when caught. With no rats or mice on the islands, it could only have eaten birds, lizards and insects.
Mr Walker urged boaties to leave their pets at home if travelling anywhere near island nature sanctuaries such as the Bay of Islands, the Poor Knights and the Hen and Chicken Islands. It put wildlife in danger as well as the pets themselves.
The cat's owners had said their pet was a poor swimmer.
In 2015 a cat named Missy fell off a yacht moored at nearby Urupukapuka Island and swam ashore.
Its owners did not tell DoC and it was not found until four months later, emaciated and with a paw stuck through its collar, when it wandered into the cafe grounds at Otehei Bay.