A missile destroyed a vehicle which the three suspects were using in the region of Sawmaa in central Baida province, the officials said.
One security official said jihadists had recently sought refugee in the vicinity following military operations against the extremists in nearby Hadramawt, Abyan and Lahj provinces.
Two suspected Al-Qaeda members were killed yesterday in a similar strike in central Marib province.
The United States has been involved in a years-long unmanned drone campaign in Yemen and is thought to have carried out dozens of strikes against what it says are members of Al-Qaeda in the Arabian Peninsula (AQAP).
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The US has vowed to continue its campaign against AQAP, which it considers to be the Al-Qaeda network's deadliest franchise.
A Saudi-led Arab military coalition that backs the Yemeni government against the Huthis has also turned its sights on AQAP, targeting it with air strikes.
The coalition is supporting pro-government forces which launched an offensive this year to retake several towns from AQAP.
More than 6,600 people have been killed in the Yemeni conflict since March 2015, the UN says.