The army raided the town, a stronghold of the jihadist network in southern Yemen, killing "three Al-Qaeda militants," a security official in Abyan said.
AFP could not independently verify the toll.
Earlier, a local official had told AFP that Al-Qaeda fighters had attacked the town.
"Al-Qaeda fighters have attacked positions of armed tribesmen" tasked with defending the town on Wednesday, and have "managed to drive them away without any resistance," the official said.
Tribesmen backing government forces in the restive region had in mid-July chased the suspected Al-Qaeda militants from Shaqra.
The security official said the army had carried out similar raids targeting Al-Qaeda positions in the cities of Zinjibar and Jaar, Al-Qaeda strongholds in Abyan.
Shaqra lies 35 kilometres (20 miles) east of Zinjibar -- the provincial capital that has been mostly under the control of suspected Al-Qaeda gunmen since late May.
The militants tried to advance to nearby villages after taking control of Shaqra but "their advance was halted by tribesmen, and clashes broke out," a tribal source told AFP.
Yemeni tribesmen have in past weeks been locked in battle with suspected Al-Qaeda militants in Abyan, especially in Zinjibar.
The army has been battling the militants calling themselves Partisans of Sharia (Islamic law), who have besieged its 25th Mechanised Brigade base in Zinjibar.
Apart from Shaqra and Zinjibar, Islamist gunmen control the village of Jaar. (*)
Editor: Kunto Wibisono
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