The Whyalla Airport could be saddled with up to $700,000 in new operational costs.
This comes after legislation relating to airports was tabled in Federal Parliament by the Home Affairs Ministry.
The Aviation Transport Security Amendment (Security Controller Airports) Regulations 2019 makes aircraft that seat 40 or more people subject to mandatory security screening.
Currently the Whyalla Airport is serviced by Qantas and Regional Express Airlines (Rex). Qantas operates two Q300 aircraft servicing the steel city which would be subject to the proposed security requirements.
Centre Alliance Senator Rex Patrick has moved to disallow the amendment, citing the potentially devastating financial impact on country airports.
"The federal government has offered the money to fund the screening equipment ... but they haven't paid for those operating costs which will be passed on to the airport," he said.
"There are two ways they can recover that - one of them is to have the councils recover it from ratepayers. The alternate and most likely option is that they will recover the cost from landing fees.
"The landing fees are charged to the airlines and the airlines are saying that a number of these routes will be put in jeopardy if those landing charges go up around the region."
During the Rural and Regional Affairs and Transport References Committee Meeting in March last year QantasLink CEO John Gissing said the costs of the new security measures would have a significant impact on Whyalla, Port Lincoln and Kangaroo Island Airports.
"We have been very clear with the government that would put in jeopardy those services entirely," he said.
Senator Patrick stressed that regional airports were the 'lifeblood' of rural communities, providing transport for the general public to access educational courses, medical services, and family.
He called on the government to "kick in" to cover the operational costs before airlines find themselves in an untenable situation in the regions.
"If the government were to do that then I would withdraw the disallowance that I have lodged in the Senate," he said.
Giles MP Eddie Hughes called on his Labor colleagues in the Senate to support Senator Patrick's disallowance move.
"I know from comments made recently there are some challenges for Rex to continue servicing Whyalla. These increased costs would just make it harder," he said.
"The government should be picking up all of these costs to not disadvantage regional areas such as Whyalla."
Member for Grey Rowan Ramsey agreed that the federal government should be tasked with covering the operational costs imposed on regional airports.
"Currently there are funds available for modifications of terminals and installation of equipment," he said.
"Given the numbers in the senate I suspect Senator Patrick's motion will have little effect. However I do concur with the view that small airports should receive consideration of ongoing assistance to meet partial costs."
Whyalla Mayor Clare McLaughlin said council welcomed the federal government's security measures but that the "ongoing running costs of the equipment should not be borne by councils or regional communities".