"While we are doing well in our efforts to move equipment out of the country ... the magnitude of the task at hand will continue to present a challenge and require significant resources in order to meet" President Obama's 2014 deadline, Austin said in an interview with the Pentagon's Armed Forces Press Service.
Prior to replacing Marine Corps Gen. James Mattis at Central Command, Austin oversaw the American pullout from Iraq in 2011.
American and allied forces have had no such luck in finding a similar exit point in Afghanistan.
"The terrain in Afghanistan is also much harsher and more difficult to negotiate," according to Austin, noting political and tribal conflicts that define the Afghan political landscape have also made things difficult for the American exit.
Ongoing political battles in Washington ahead of a looming government shutdown are also posing serious challenges to the U.S. effort to end the war in Afghanistan.
DOD operations to prepare U.S. troops heading to Afghanistan are part of the department's slate of exempt activities under a government shutdown.
Aside from combat operations in Afghanistan and elsewhere, other exempted missions range from ongoing intelligence operations to maintaining dining halls and gyms, according to a mission list released by the Defense Department on Friday.
While troop deployments to Afghanistan will not be affected, operations to get American service members home from Afghanistan may not be exempt.
Those troop withdrawals may be suspended under a shutdown, since those missions technically are not supporting ongoing operations in country, Pentagon Comptroller Bob Hale said Friday.
“That is a judgment Gen. [Joseph] Dunford will have to make" on how to get those troops home, if a shutdown occurs, Hale said.
Dunford is the top U.S. commander for all American and coalition forces in Afghanistan.
However, Austin said the U.S. withdrawal plan from Afghanistan remains on schedule, due in part to lessons learned from the Iraq pullout.
"We were successful in conducting the transition from Iraq, and we are now doing a good job of applying the knowledge and experience gained there toward efforts in Afghanistan," he said.