The Dunedin City Council encouraged businesses to discard food that could be contaminated, and make an insurance claim to cover the cost.
O'Leary said Emerson's was looking into its insurance cover, but the size of its excess meant the company would be lucky to get money back.
"I'm plucking a figure out of the air but I'd estimate this has cost us maybe $50,000 to $100,000," he said.
"Probably around the $60,000 mark.
"Someone made a mistake. And that mistake has cost Dunedin businesses an awful lot of money so it was an error, which is a bit more difficult to swallow.
"We'll see over the next few weeks how it all pans out."
The restaurant run by Emerson's is open again but the company hasn't brewed since Tuesday morning.
O'Leary said the brewer hoped to slowly start up production again tomorrow, but it would be a while before it was at full steam again.
"We don't carry stock, so basically we will never catch up on this week because we make what we sell," he said.
"So if we lose a week, we lose a week unless you put your guys through hell to catch up - which we're not going to do."
He said the company wouldn't run out of beer, but the week's delay meant it wouldn't grow quickly over the month either.
Despite this, O'Leary said the situation could have been a lot worse had the council not acted as quickly as it did.