The militants attacked a checkpoint near the Shabwa province village of Bayhan with automatic rifles, also wounding a number of soldiers, the official said.
The army has been engaged in a major ground offensive against Al-Qaeda in Shabwa and neighbouring Abyan province in a bid to expel it from smaller towns and villages that escaped a previous sweep in 2012.
Troops have entered a series of towns but analysts say the advances could be the result of a tactical retreat by militants in coordination with local tribes.
Al-Qaeda took advantage of the collapse of central authority during a 2011 uprising that forced veteran strongman Ali Abdullah Saleh from power to seize large swathes of the south and east.
The jihadists remain deeply entrenched in Hadramawt province further east where they have carried out a series of spectacular attacks in recent months.