Three were killed and six wounded in the coastal town of Shaqra, seized by Islamists in August, during an air strike, the official said.
Another three were killed and dozens wounded in Zinjibar, which was captured in May, when Yemen army forces shelled one of their bases in the northern part of the city.
Two soldiers were wounded during clashes with the militants, the official said.
Islamist militants have also been in control of Jaar since March, apparently exploiting a security vacuum while President Ali Abdullah Saleh fights to keep his grip on power after nine months of protests against his rule.
Saleh has refused a Gulf-brokered power transfer plan three times, aggravating protests and bringing the impoverished country to the brink of civil war.
