Only 28 per cent reported an increase in business, and nearly 60 per cent reported a drop in the number of domestic visitors with only 14 per cent experiencing a rise.
"Any motel with a commercial or domestic component around it has struggled, and certainly around the South Island it's been really quiet."
Mr Baines said overall business had been about 20 per cent down on the same period last year, and estimated that to be between $15 million and $25 million in turnover losses.
Auckland mother of two Lisa Boyd, who usually takes her family on a New Zealand road trip during the spring break, will not be doing so these school holidays.
"It's probably a once-in-a-lifetime experience to have the Rugby World Cup here, and it just makes more sense to enjoy the rugby festivities in Auckland than to be driving around the country," said Mrs Boyd.
Neil Barker, owner of Manukau Motor Lodge, said he increased accommodation rates by about 18 per cent, hoping for a cup windfall, but instead suffered a "rather significant" drop in bookings.
"The corporates are staying away and the locals are not travelling, so we have been left with vacancies throughout the competition period."
Mr Barker said more fan zones should have been set up in areas outside the central city to ensure a more even distribution of fans, so motels outside the main centres would not suffer.
But the Motel Association remains optimistic that things will go right for motels in the long term.
"In all major sporting events, even the likes of Fifa World Cup, there's always an expectation it's going to be full, but the reality is that it never is," Mr Baines said.
"I think the Rugby World Cup has made New Zealanders see the country through the eyes of international [visitors], and realise what a fantastic place this is, and hopefully it will stimulate them to travel around New Zealand in future."