Nicky Atkinson of project Piopio Trust said the flags in the small township, 25km south of Te Kuiti, had been up for two weeks.
She said the trust and members of the community had also worked hard to beautify their town for the tournament, painting the public toilets black and decorating them with silver ferns and lining the main street with 600m of triangular flags.
"People are rather brassed off," said Ms Atkinson."We've gone to quite a bit of effort so when someone comes along and does something like that it is disappointing.You would hope that people would see the kind of effort we've put in to get these things down."
Otorohanga Business Association president Anne Laws said the thefts in her town were disgusting and heartbreaking.
She said the flags cost businesses several hundred dollars and had lifted the town's spirit. Locals and visitors had enjoyed seeing them.
"Personally I'm livid ... the town is quite horrified that there could be one or two people who have done this, we are just not pleased, not impressed at all."
Otorohanga mayor Dale Williams believed the thefts were not done by a local resident and could have been due to "someone wanting a souvenir".
"It's left a bit of a sour taste but we will replace them and get on with it."
A staff member at Otorohanga police said about five of the missing flags had been handed in to police.