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 yesterday 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.
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 jihadists 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.
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.
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