Rex Airlines will no longer service the Adelaide to Whyalla route from Saturday despite a confirmed extension of airport security screening funding from the federal government.  

Whyalla City Council was contacted on Thursday afternoon confirming a three-month security screening funding extension. 

"We received advice that we've got a temporary or small extension to the funding that we've been receiving over the last couple of years that has been covering the cost of security screening," Whyalla City Council chief executive Justin Commons said. 

"That will mean we will not need to pass on the cost of security screening to both [Rex and Qantas] airlines until now the end of September at the earliest." 

The federal government formerly funded the transport screening cost of $35 per passenger but announced this would stop from July 1. 

In a media release dated May 18, Rex Airlines declared they would exit the Whyalla to Adelaide route from July 1. 

It sited the security screening charge of $35 to $40 per passenger which would have to be covered by the airline as the reason they would stop servicing the route. 

"The significant additional security cost makes the Whyalla to Adelaide route unviable for Rex and as a result of Council's decision Rex has no option but to exit," Rex General Manager of Network Strategy Warrick Lodge said. 

Despite multiple attempts to contact Rex Airline's media team on Friday, they did not respond to requests about whether the decision to cut services from Whyalla to Adelaide would be reversed as a result of the funding extension.

On the Rex Airlines website on Friday, no flights were available on the Adelaide Whyalla route from July 1. 

In correspondence from Federal Minister for Infrastructure, Transport and Regional Development Catherine King to the Whyalla Council, she said it remained a longstanding position of successive governments that industry was responsible for managing security screening costs. 

"Whether those costs are passed on to passengers and what form they may take, is a commercial matter between airport operators and airlines," Ms King said in April.

History between council and airline

In May, Rex Airlines slammed the Whyalla City Council as being devious by trying to get the airline to cover the screening costs charge. 

Whyalla Mayor Phil Stone fought back, and said the airline was using the council as a scapegoat for its own decisions. 

Qantas, which agreed to increase services to the area, continues to service Whyalla as its only airline.

Mr Commons wrote to both airlines on Thursday night advising them of the dropped screening costs for the next three months. 

"Rex had made a very clear decision to withdraw from the Whyalla route, we're obviously disappointed that they made that decision but we understand they need to make their decisions based on the commercial viability of the route," Mr Commons said. 

"Because we don't have the passenger volumes that the major cities have, we end up paying a disproportionately higher cost for security screening per passenger.

"Clearly the system's not working and we need to find a better solution."