The Governor's flag, originally instituted by the Admiralty, was intended for maritime use exclusively. Prior to 1874 colonial Governors possessed no official flag and there were no clear-cut rules in the matter. In 1874, however, the Admiralty directed that colonial Governors should fly, when travelling at sea, “the Union Jack, with the arms or badge of the colony emblazoned in the centre thereof on a white shield surrounded by a green garland”. Sir James Fergusson announced in the Gazette that the badge to be worn in the Union Jack used by the Governor of New Zealand when he embarked in any vessel “shall be the Southern Cross as represented by four five-pointed red stars emblazoned on the white shield aforesaid, and the monogram ‘NZ’ in red letters in the centre of the Southern Cross”. Succeeding Governors found it convenient to use this flag on shore and it became accepted as the official vice-regal flag (A17). In 1907, following New Zealand's promotion from “colonial” to “Dominion” status, New Zealand ministers asked that the garland of laurels should be replaced by one of fern leaves. With this alteration, the flag continued to be used by successive Governors until about 1935.

In January 1931 a new vice-regal flag was designed, partly in order to meet South African objections to the use of the Union Jack, and partly to symbolise the Governor-General's new status as the King's personal representative. This was a uniform design for all Dominions and consisted of a “Royal blue ground on which is the Royal Crest in gold, with the name of the Dominion in gold beneath”. As neither Lord Bledisloe nor his ministers were sympathetic to the change, the flag was not flown until after Lord Galway's arrival.

The Governor-General's flag (A18) occupies the same position in New Zealand that the Royal Standard does in England. It is the personal flag of the Governor-General for the time being; it is flown on all occasions when he is present and over Government House when he is in residence. Whenever the Governor-General's office falls vacant, or is vacated, the Administrator of the Government is entitled to fly the Governor-General's flag. The deputy of the Governor-General uses the New Zealand Ensign.