According to its website, the service stopped on April 6, "as there are no longer facilities to lodge freight" at the regional airport.

Co-founder of Pambula-based seafood supplier South Coast Sea Urchins Ryan Morris said he shipped nationally three times a week from Merimbula.

"I don't know where it leaves us to be honest," he said. "I'll put it this way, we have stopped production this week because I can't get product out.

"It hasn't had a small impact, it's had a massive impact."

Despite using Qantas Freight for about 15 years, Mr Morris said he had received no correspondence from the company explaining why the service was cancelled.

"We were dropping products at the airport that day and they told us that we couldn't put it on the plane - that's how we found out," he said.

"We've got a time-sensitive product - perishables - that can't sit around waiting for trucks, we need to be able to get it on a plane.

"We send products all over the country - to Darwin, Brisbane, Melbourne, Perth, Adelaide and we heavily relied on that service and now they're just turned it off."

It was a similar situation for director of Tiny Zoo Steve Sass, who said he used the outgoing freight service from Merimbula Airport at least once a week.

"No-one gave us any indication it was happening or why," Mr Sass said.

"It's very disappointing. It's going to hurt a lot of people, a lot of businesses here."

Mr Sass said his zoo operations used freight services across the country "as regularly as any zoo does".

"Air freight connects zoos quite efficiently, it enables zoo populations to be managed and animals moved around for genetic diversity - it's vital for threatened species breeding programs," he added.

Mr Sass said the check-in staff at the airport had always been "fantastic" and that nothing appeared to have changed regarding the number of flights in and out of Merimbula.

"We can still operate, but it makes it much harder.

"If someone said tomorrow a 10-tonne limit was being placed on Brown Mountain so trucks couldn't drive it, everyone would be up in arms.

"I don't understand what it's costing them."

Despite an assurance from Merimbula Airport that the airline would be in contact, Mr Morris from South Coast Sea Urchins said he had no idea if the freight service was on hiatus or the cancellation was permanent.

In the meantime he was scrambling to find alternative services to freight his products.

"I've got a lot of trucks that can go to Melbourne and Sydney but I've got product that goes to Darwin and Brisbane and it's just really difficult," he said.

"My factory is only 150 metres from the airport and now I'm going to have to drive my products up to Moruya."

Road freighting the products to Moruya will add extra cost to his business Mr Morris said and importantly, extend the time taken to reach customers.

A spokesperson for Bega Valley Shire Council said Qantas could provide further comment on its commercial decision to stop the outgoing freight service. But that it wasn't related to the draft airport masterplan.

"There are a range of other freight providers that operate out of Merimbula Airport that will continue to support exports from businesses in the Bega Valley," the spokesperson said.

"The decision by Qantas is not related to the recently exhibited draft Merimbula airport masterplan or the general aviation precinct works.

"However, this decision by Qantas does reiterate the importance of investing in updating council's airport masterplan. Our goals for the airport need to be clear so that businesses can plan for their future growth."

Qantas and Merimbula Airport freight managers have been contacted for comment.