"Security forces have taught the terrorists of al-Qaeda a hard lesson and inflicted painful hits on them, forcing those terrorist elements that tried to hide, to flee after dozens were killed and wounded," al-Zouari said.
Earlier reports about the violence in Loder, 250km southeast of Sanaa, the capital, indicated the clashes were between the military and townspeople.
The reports could not be independently verified.
An AFP news agency tally based on official and medical sources had put the total death toll on Tuesday at some 33 people, including 19 fighters, 11 soldiers and three civilians.
Other security officials in Abyan also said that al-Qaeda's fatalities were 12, and that all were Yemenis, Saba news agency said.
Authorities had said that Adel Saleh Hardaba, 27, whom they described as the al-Qaeda second-in-command in Loder, was among the dead.
The army had at that start of the fighting distributed pamphlets urging civilians in Loder, which has a population of 80,000, to leave.
Security officials told the AFP at the weekend that civilians had mostly fled the city and that "only gunmen are left".
Many of the fighters were believed to be foreigners, notably Saudis and Pakistanis.
South Yemen, and Abyan province in particular, is feared to have become a base for al-Qaeda fighters to regroup under the network's local franchise, Al-Qaeda in the Arabian Peninsula (AQAP).
Largely tribal Yemen is the ancestral homeland of Osama bin Laden, the al-Qaeda chief.
Yemen has intensified operations against AQAP since December. The network has claimed responsibility for a December 25 attempt to blow up a US airliner over Detroit.
US officials cited by the Washington Post on Tuesday have warned that the threat of al-Qaeda's branch in Yemen to US security has become higher than that of the core group based in Pakistan, recommending escalating US operations against AQAP.
In addition to fighting al-Qaeda-linked groups, Yemen's government is battling a separatist movement in the south and a Shia uprising in the north.