The federal government will again subsidize airline flights between Macon and Atlanta, with the U.S. Department of Transportation awarding a nearly $2 million annual subsidy to Sun Air International to take over the route.

But Macon’s eligibility for the subsidy - which in the past has amounted to hundreds of dollars per passenger - isn’t set in stone. Under reforms to the subsidy program, Macon must maintain an average of at least 10 passengers boarding planes a day to continue under the program.

The DOT said it “will continue to monitor Macon’s eligibility” for the Essential Air Services subsidy. Communities can lose subsidized air service if the annual subsidy amounts to more than $1,000 per passenger.

The DOT said it “strongly encourages” Macon and Sun Air to work together to increase passenger counts.

The subsidies are intended to ensure adequate air service to small and mid-sized cities by providing a guaranteed revenue supplement to carriers.

The current carrier on the 80-mile Macon-Atlanta route, GeorgiaSkies, previously received the subsidy but last year started operating the flights without government help. Fares went up and passenger counts plummeted, to the point where an average of three passengers boarded the flights a day from Macon to Atlanta in fiscal year 2011.

In April, GeorgiaSkies told the DOT it planned to drop the business, prompting the agency to seek a new carrier.

Of two proposals, the DOT this week selected Sun Air to operate the service with nine-passenger planes for two years. Sun Air plans to fly the route four times each weekday and twice a day on weekends.

Meanwhile, Athens is also set for a change in its subsidized airline service.

GeorgiaSkies operates flights from Athens to Atlanta with a roughly $1 million annual subsidy. The DOT collected four proposals for the next carrier to operate subsidized flights from Athens after GeorgiaSkies’ contract ends, and a decision is pending.

GeorgiaSkies did not submit a proposal for Athens service, with chief executive Greg Kahlstorf saying the subsidy program “doesn’t seem like a good long-term business model.”

If Athens leaders get their way, the college town’s airport will have federally-subsidized flights to Nashville and Charlotte, but no longer to Atlanta.

Nashville and Charlotte are the route options from Athens raised by SeaPort Airlines, and SeaPort’s was the proposal supported by Athens’ Airport Authority and Mayor Nancy B. Denson.

In a letter to the DOT, Denson discussed the potential success of flights to the music city of Nashville, invoking Athens’ own music heritage as “the birthplace of bands such as the B-52’s, REM, and Widespread Panic.” Charlotte, meanwhile, is a hub for US Airways.

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An average of fewer than three passengers a day boarded GeorgiaSkies’ 72-mile flights from Athens to Atlanta last year — below the 10 passenger minimum.. The Athens-Atlanta route — like the Macon-Atlanta route — is so short that some travelers choose to drive rather than fly.

“For this market to remain viable in the long term, something different has to happen there,” said SeaPort vice president Tim Sieber after the company submitted its proposal. “The world has a love-hate relationship with the Atlanta airport.”