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 assault came hours after a drone strike killed three al Qaeda suspects late on Wednesday as they were travelling in a vehicle in the Wadi Abida area, east of Sanaa, tribal sources said.
The United States is the only country operating drones over Yemen, but US officials rarely acknowledge the covert operations.
The drone programme has been defended by both the White House and Yemeni President Abdrabuh Mansur Hadi, in the face of protests by human rights groups over the civilian death toll.
Washington regards the jihadist network's Yemen affiliate, al Qaeda in the Arabian Peninsula (AQAP), as its most dangerous and has stepped up drone strikes against its leaders this year.
Around 60 suspected militants were killed in a wave of strikes against suspected AQAP bases and training camps in mid-April.
The strikes came shortly before the Yemeni army launched 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 backed by militia have entered a series of towns but analysts say the advances could be the result of a tactical retreat by the 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 jmilitants remain deeply entrenched in Hadramawt province further east where they have carried out a series of spectacular attacks in recent months.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ