They will fly in the front of the Featherston Library on Fitzherbert St, in front of the old Greytown Library, now the Design Library, on Main St and in front of the SWDC office in Kitchener St, Martinborough.
In Carterton, due to the three flag poles not standing in line, the two flags are "about 15 metres apart".
"They are flying, just not side by side," said council community development manager Carolyn McKenzie.
The current New Zealand flag is flying outside the library and the proposed Silver Fern Flag is outside the Carterton Events Centre.
"Obviously we don't have a preference and it is up to the public to decide," Ms McKenzie said.
"But I do think changing the flag is going to be an emotive subject for some people."
Herald columnist Brian Rudman said "fold up the old one and send it back to the British Navy", while Jim Hopkins, another Herald columnist, said "let the flag remain".
"They recall mistakes and triumphs, failings and virtues" Hopkins said.
If New Zealand votes for a new flag, it is likely that the change would take place within six months of the second referendum.