Arabica coffee beans are what keep the cafes around Australia churning out $3 coffees, but that coffee could soon come with an extra jolt.

Wholesale coffee prices are higher now than ever before. And while the industry is absorbing the extra cost for now, consumers are being warned of a price shock to come.

Rabobank senior analyst Wayne Gordon says the price of coffee beans has hit a 12-year high on the New York Futures Exchange because of heavy rainfall in Brazil and surrounding countries.

"Of course that's tightened up supply and that's what's given the market that little bit of jump," he said.

Wayne Fowler has been monitoring the price of coffee in Australia's capital cities for several years, in what he calls the "Cappuccino Price Index", or CPI.

"[The CPI] monitors what everyday Australians [are] paying for their humble cup of coffee every day," Mr Fowler said.

"Takeaway coffee I've been seeing... the norm is between $3.40 to $3.50. Our CPI comes in a little bit lower than that because a lot of people do buy takeaway and they get their discount cards and end up paying a little bit less."

One company not at the mercy of global coffee prices is Saint Ali Coffee Roasters in Melbourne. It buys premium coffee which can be sold for as much as $12 a cup.

Saint Ali's Salavatore Malatesta says most other coffee retailers would be absorbing the extra costs.

"Coffee prices have gone up but what hasn't gone up is the retail price of coffee," he said.

"If you take out GST most retailers are selling coffee at about $3.30 or less a cup which is sort of the same as some of the prices we were fetching 10 years ago.

"I think it's made it much harder for your standard cafe operator to turn a margin."

While the price of beans is through the roof now, supply is expected to be much better next year. So the pain for coffee merchants may only be temporary.

Wayne Fowler says the cost of the beans in an average cup is only 20 cents, but he would not be surprised to see retail prices rise anyway.

"It's also an opportunity where people can add on all the other costs, rising costs of business," he said.

"We're starting to see rents increasing in the market place, certainly wage costs, there's big wage costs to get passed through to people and this could very well be the trigger that will allow people to get through a price rise."