Scottish Borders councillor Vicky Davidson said there was no good reason, apart from Mr Scott's connection to the area, for the flag to remain.
"There is a strong spiritual, social and political case for the flag to be repatriated to New Zealand.
"We have been reassured that this artefact will be carefully conserved, displayed and interpreted in the museum and I hope my fellow councillors will support the repatriation of the flag."
The request from Wairoa Museum director Mike Spedding was accompanied by three letters from descendants of key figures in the battle.
Three came from descendants of noted Maori leaders, and one from a descendant of Ihaka Whaanga, who fought alongside Crown forces, and is said to have captured the flag.
The letters said the flag's return could be a symbol of the resolution of social, economic, political and spiritual turmoil for Maori.
The cost of repatriation will be met by Wairoa Museum.