A federally-subsidized airline route between Atlanta and Macon has hit more turbulence.

The airline set to take over the flights with a $2 million annual federal subsidy has decided to withdraw from the market. Fort Lauderdale-based Sun Air International was chosen by the U.S. Department of Transportation in September but said it has had “greater challenges than anticipated” and will concentrate on other markets.

The current carrier on the route, GeorgiaSkies, told the DOT last year it wanted out of the market, after it saw passenger counts plummet to an average of three passengers boarding flights each day from Macon to Atlanta in fiscal year 2011.

The federal Essential Air Service subsidies at one point amounted to $464 per passenger on the roughly 80-mile Atlanta-Macon flights, which often took off nearly empty, leading to scrutiny of the government-supported route.

In light of Sun Air’s withdrawal, the DOT plans to solicit a new carrier. GeorgiaSkies will continue to operate the flights until a replacement is found.

Sun Air started federally-subsidized flights in other markets and had delayed its start-up date for Macon until this month.

Now, Sun Air says challenges with pilot recruiting and training and establishing maintenance bases led it to decide to concentrate resources on other markets and withdraw from Macon — before its service there even started.

“We apologize for any inconvenience and additional work that this requires for the Department, but believe it to be the right decision for all parties involved,” un Air president David Hackett wrote in the memo to the DOT.