The government claimed on Saturday that the air raid, which took place on Friday, killed Qasim al-Raymi, the Yemeni al-Qaeda wing's military chief, as well as Ayed al-Shabwani, who is accused of sheltering al-Qaeda fighters at his farm in the eastern province of Maarib.
It identified the other men as Ammar al-Waili, Saleh al-Tais, Ibrahim Mohammed Saleh al-Banna. The sixth person was unidentified.
Muttahar al-Masri, Yemen's interior minister, has vowed further strikes on al-Qaeda, state media said.
"These strikes will not be the last so long as the security and stability of the country and its institutions is targetted by terrorist elements," the Yemeni defence ministry's online "September 26" newspaper, cited al-Masri as saying.
Yemen has come under increased pressure to stamp out the al-Qaeda in the Arabian Peninsula, a group formed from Yemeni and Saudi affiliates of al-Qaeda, after it claimed responsibility for the failed December 25 plot to bomb a US-bound passenger aeroplane.
The government launched several attacks on al-Qaeda
Yemen gained a reputation as an al-Qaeda "haven" after the September 11, 2001 attacks in the US, and came under the spotlight again after crackdowns on the group in Pakistan and Afghanistan raised fears Yemen could become a training and recruiting centre for fighters.
As well as tackling al-Qaeda, the Yemeni government is fighting the so-called Houthi rebel group in the country's north and a secessionist movement in the south.