During the Second World War (1939-45) the island was part of the Auckland Harbour defences. The day after war broke out, 12 Royal Naval Volunteer Reserve signalmen landed on Tiritiri Matangi to identify all approaching vessels. The Navy duplicated much of the Auckland Harbour work of identification. At first, the two services shared the Auckland Harbour Board facilities but it soon became apparent that the Navy needed its own building.

The military then built the Port War Signal Station, near the lighthouse, linked to gun emplacements on Whangaparaoa, Rangitoto, North Head and Waiheke Island. The Port War Signal Station had a view from Kawau Island past Aotea Great Barrier and the Coromandel to Auckland but, significantly, the Tiri channel was obscured. Ships at sea were forbidden to use their wireless in wartime, so communication with them was by flags, semaphores or Aldis signal lamps.

After the bombing of Pearl Harbour (7 December 1941), the US poured money into New Zealand’s defences and the Army established a Fortress Observation Post on Tiritiri Matangi. The Army rebuilt the Fourth House, concreting the outside and adding a concrete tower. The Fortress Observation Post gave information to the nine-inch guns on Whangaparaoa Peninsula and controlled the mines in the Tiri channel. Mines were laid across the Tiri channel and out to Rakino Island and The Noises. These mines exploded when struck by a ship.

With the arrival of the Army, the Auckland Harbour Board signalmen were withdrawn, leaving one man as custodian of the foghorn and radio beacon.

The Hobbs family (who held the Tiritiri Matangi farm lease) had taken their stock off the island in 1940, donating a cow to each of the services. Without the stock the grass grew higher and the kiore rats increased to plague numbers. High-voltage electric fences were rigged around the Fortress Observation Post, and a small light on the wall would light up every time a rat was zapped. This did kill thousands of kiore although it didn’t make a dent in the population. The Navy then tried a more low-tech solution, a tom cat.

Despite all the upheaval, the six years of military presence on Tiritiri Matangi had little effect on the island’s ecology. Anne Rimmer wrote in her book that the effect was probably more influential in the increased awareness of Tiritiri Matangi in the minds of the people who would guide the island’s future path. Also significant for New Zealand as a whole were the widened horizons of the thousands of servicemen and women who had served overseas.

In 1945 the three signalmen from the Auckland Harbour Board returned to Tiritiri Matangi. A year later Hobbs’ stock returned. The lighthouse keepers returned in 1947 and Auckland Harbour Board closed the signal station.