The FAA intends to propose regulations that would require the largest operators of public air charters to adhere to the same requirements as commercial airlines.
Such a change could significantly impact JSX and other charter operators with a similar business model.
Regulations also could affect SkyWest, which is vying for approval to form a subsidiary that flies commuter public charters.
Carriers operating under public charter authority must limit their flights to no more than 30 passengers. But they aren't subject to the 1,500-hour flight-training rule for pilots that commercial airlines must follow. Also, charter pilots aren't subject to the mandatory retirement age of 65 for commercial pilots.
And, customers don't have to go through the normal airport TSA security screening. That has allowed JSX to grow while operating out of private airport terminals, where customers can arrive less than 30 minutes before their flight.
JSX says it serves 23 airports, and the company flies 43 routes according to a June public filing.
SkyWest, meanwhile, applied last summer for permission to fly scheduled commuter flights in small markets as a charter operator. Unlike JSX, SkyWest says the subsidiary would operate at commercial airports and adhere to the same flight-training requirements as commercial airlines. SkyWest's existing on-demand charter service does use pilots over age 65.
Another sizeable public charter carrier is Contour Airlines, which flies regional commuter routes and interlines with American Airlines.
In a statement, the FAA noted that public charter flights have expanded in frequency and complexity in recent years.
"This rapid growth poses an increased risk to safety if left unchecked," the agency said.
The FAA announcement drew quick praise from the Air Line Pilots Association, which has opposed the SkyWest Charter application and in recent months has joined with other airline industry unions and American Airlines in arguing that the Biden administration should crack down on JSX and its business model.
"Some airlines use the public charter loophole to cut costs by skirting lifesaving safety rules," ALPA president Jason Ambrosi said.
JSX called the FAA's notice "disappointing" and said it would actively participate in the planned regulatory review process.
"JSX complies with all applicable rules and regulations and far exceeds the safety requirements germane to our public charter operations," the carrier said. "As a beacon of American innovation, we're confident that JSX can and will model the way forward to ensure safe, reliable and accessible air travel for all."
SkyWest, meanwhile, said that the FAA's plan to review the overriding rules for public charters should clear the way for the Transportation Department to approve its commuter air carrier application, since big-picture issues related to the regulations will be dealt with by the FAA. SkyWest's application has languished since last June.
SkyWest said its charter division "already exceeds current safety requirements and will transition to any additional requirements that may be adopted by the FAA as part of the rulemaking process."
CORRECTION: A previous version of this article incorrectly stated that Tradewind Aviation and Tailwind Air would be affected by the new regulations. These companies operations under a separate authority.