Maritime New Zealand said in a statement it would take about 24 hours to get to the vessel.
"HMNZS Wellington was the closest available vessel with the necessary medical capability on board to assist the injured crewman, and is not currently required for the Whakaari/White Island response."
The Navy vessel left White Island about 2.15pm.
Meanwhile, the Police Eagle helicopter searched Taungawaka Bay this afternoon for any sign of the two bodies still missing following last week's eruption on Whakaari.
Police have so far confirmed 16 people have died.
The 16th person died on Saturday after being repatriated to Australia.
One week on, 14 people remained in hospitals across New Zealand, while another 13 people had been transferred to Australia.
Two people remain unaccounted for on or in the vicinity of Whakaari/White Island.
The weather around the island today has hampered search efforts for the pair, preventing an earlier search by Eagle and a shoreline search by boat.
Police said they would continue to focus on areas from White Island through to the East Cape based on tidal patterns and as the weather allows.