There are calls for the federal government to make security funding for country airports more equitable after Rex Airlines cancelled its service in a regional South Australian city.

A government subsidy on security screening in airports is set to end by July, meaning councils will have to foot the bill or pass the cost onto airlines.

In SA, Lower Eyre Peninsula Mayor Jo-Anne Quigley said that would mean a greater financial burden on country airports with fewer passengers, but sharing the cost of security screening across all airports would reduce the cost significantly.

She said her council's financial calculations showed that a 75 cent levy per passenger per flight nationwide would cover the costs of security screening at all regional airports, including Port Lincoln's.

"At the moment our screening costs are about how many passengers leave a particular airport, so if that became Australia-wide this wouldn't be a financial burden on anybody," Cr Quigley said.

Last week Rex announced it would be cancelling its Whyalla to Adelaide flights because Whyalla City Council was attempting to charge the airline a security screening fee of $35-$40 per departing passenger.

In recent years the federal government announced that body and baggage scanners would need to be installed at regional airports.

It initially proposed the cost be picked up by airports before agreeing to offset the additional expense with funding, which was announced in 2020.

'Do the right thing'

SA Labor politician and Member for Giles Eddie Hughes accused the federal government of "dropping the ball" on regional air travel.

"The federal government needs to intervene and do the right thing," he said.

But a Department of Home Affairs spokesperson said airports were responsible for managing the costs of their security obligations.

"The responsibility of airports to meet and manage the costs associated with security screening is a long-standing policy of successive governments and is a key pillar of Australia's aviation security framework," they said.

Grey MP Rowan Ramsey, whose electorate includes Whyalla, has also called for a national levy to be charged on all flights to pay for airport security requirements.

"Airline security across the nation is a national responsibility and it should be funded by a national levy across all flights and not heaped onto regional flights," he said.

Cr Quigley said she planned to introduce a motion at the upcoming national general assembly of the Australian Local Government Association calling on the federal government to change the legislation so that all airlines have to pay for security screening.