Many Māori in the 19th century saw the Union Jack as a potent symbol of Great Britain's power in New Zealand. In the New Zealand Wars, Māori parties who sought to resist government forces often devised their own flags to show their independence and counteract the 'mana' of the Union Jack.
The King Movement used three flags, bearing the words 'Kīngi' (King) and 'Niu Tireni' (New Zealand), for the appointment of Pōtatau Te Wherowhero as the first Māori King in 1857. The tradition continued with the crowning of Tāwhiao in 1861, and all successive monarchs have had their own personal flags drawn up for use at the residence at Tūrangawaewae, and when visiting other maraes which accept the monarch's authority. The monarch's flag is considered to be strictly tapu and is kept by a hereditary custodian until interred with the monarch upon death.
The Pai Mārire or Hauhau faith also believed in the power of flags, with the 'Niu Pole' and its three flags prominent in religious ceremonies. The 'Riki' flag or pennant was a war flag, while the 'Ruru' flag represented peace. The relative positions of 'Ruru' and 'Riki' on the Niu pole were believed to indicate whether the spirit behind the gathering was peaceful or hostile. The third flag used on the pole was the personal flag of the priest conducting the ceremony.
Te Ua Haumēne, the leader of the Pai Mārire movement, also had his own personal flag, which featured the word 'Kenana' (Canaan) to show that he identified with the Jews. The five apostles of the church also had personal flags decorated with various distinctive symbols, such as crosses, stars and crescents.
Te Kooti's use of flags in the New Zealand Wars is also notable, with the designs of each flag being altered as his success or failure dictated. Perhaps his most famous flag is that dubbed 'Te Wepu' (the whip), made for Ngāti Kahungunu by nuns at the Greenmeadows Missionary School. Measuring 52 ft by 4ft (or just under 16m by 1.2m), it was captured by Te Kooti in 1868 and remained in his possession until reseized by Gilbert Mair near Rotorua in 1870. Te Wepu was decorated with a crescent moon, a cross, a six-pointed star, a mountain representing New Zealand and a bleeding heart, thought to symbolise the sufferings of the Māori people. The fate of Te Wepu is unknown, but there are stories of it having been used as a duster, cut up or stolen from the Dominion Museum.
Flags were also used to reward or thank Māori who supported the government during the New Zealand Wars, with the government continuing this tradition as a mark of recognition in the early 1900s. The British or New Zealand Red Ensign with the name of the hapu or a notable ancestor worked into the design was a common gift from either Queen Victoria or the government, as the colour red was often preferred by Māori for its properties of 'mana' or rank. The customary use of the Red Ensign by Māori on significant occasions is still provided for in the Flags, Emblems and Names Protection Act 1981.
Other groups had tribute paid to them with flags of different designs, such as that presented by the ladies of Whanganui to the lower Whanganui iwi in 1865 to mark their success at Moutoa Island. Today the Moutoa flag is believed to be held at the Whanganui Regional Museum.
Imperial and colonial troops also had their services recognised with flags. The Taranaki Militia and Rifle Volunteers' efforts in 1860 were rewarded by the presentation of an impressive flag in 1861, designed and sewn by the women of the area.