Regent Theatre Otago Trust chair Alison Cunningham said it had a standing arrangement for another organisation to come and collect unsold books at the end of the sale.
The trust had been obligated to remove any remaining items from the Edgar Centre venue by the end of Sunday, March 3, but had found out about lunchtime that the books would not be collected.
The situation had been "extremely frustrating", Ms Cunningham said.
She declined to name the other organisation as she did not want to blame them for the issue.
"We don’t throw anything away if we can avoid it, because by the time it’s got to the sale, we’ve already decided that it’s saleable.
"Obviously we spend a lot of time and energy on organising all this stuff, so the last thing we want to see is it thrown away, but in these circumstances we didn’t have any other choice."
Only books which had been out on tables were discarded.
The trust wanted books to go to a good home and tended not to reuse books which had already been displayed, as they wanted people to feel there was a new selection each year.
This year’s book sale marked 41 years of the event.
Waste had been a problem for the book sale since its start, but over the last decade there had been work done to prevent it — although the trust was still reliant on other organisations.
The trust was always interested in talking to groups which would be keen to take books off their hands, but they had to understand there were tight deadlines, Ms Cunningham said.
While she was not sure of the exact amount of books disposed of, the Otago Daily Times understands three one-tonne skips were disposed of.
That amount would not come as a surprise.
The event had otherwise been a success and was the third-highest grossing book sale yet.
There had been positive feedback about the Edgar Centre as a venue, which was more accessible for bookworms with mobility issues, and it was likely it would be used again in the future.
The trust was grateful to the volunteers and people who donated items, as their efforts made operating the Regent Theatre possible.