The interior ministry said Al-Qaeda in the Arabian Peninsula (AQAP) military boss Qassem al-Rimi died when a missile hit his vehicle in the eastern part of Saada province on Friday.
Also killed were Ayed al-Shabwani, Ammar al-Waili, Saleh al-Tais, Egyptian Ibrahim Mohammed Saleh al-Banna and an unidentified sixth person, the ministry said in a statement on its website.
There had been conflicting reports about the identities of those killed when a warplane targeted a three-vehicle convoy, with one report on Friday saying that Waili and Tais had escaped.
Rimi was among 23 people who had made a daring escape from a state security prison in Sanaa in February 2006 that left the Yemeni government red-faced, and he was on a list of 152 wanted suspects.
Banna, also known as Abu Aymen al-Masri, was said to be an "ideologist" of the group.
Meanwhile, the defence ministry announced the arrest on Saturday of three suspected Al-Qaeda members in the northern area of Alb, near the border with Saudi Arabia.
It named them as Ahmed al-Razehi, Yasser al-Zubai and Ahmed al-Heemi, and said they were wearing military fatigues and had guns and explosives.
Saturday's arrests were the latest in a series of blows since late December, when the government launched its latest campaign against Al-Qaeda.
On Tuesday, security forces killed Abdullah Mehdar, said to be the group's kingpin in Shabwa province, east of the capital.
Provincial Governor Ali Hassan al-Ahmadi said dozens of fighters, including Saudis and Egyptians who had fled Afghanistan, were holed up in Shabwa.
Among them, he said, were current AQAP chief Nasser al-Wahaishi, his Saudi number two Saeed Ali al-Shehri and radical US-Yemeni cleric Anwar al-Awlaqi.
Yemen Post newspaper reported on Saturday that the radical US-born Awlaqi, who may be linked to the botched Christmas Day plane bombing of a US-bound airliner, is living in south Yemen under Al-Qaeda protection.
"My son is alive" in Shabwa province, Awlaqi's father Nasser told the newspaper. "He now probably has some Al-Qaeda members protecting him because they are from the same tribe, and not because he is an Al-Qaeda member.
"Anwar is a moderate Muslim. He believes in the principles of Islam. He is not an extremist," his father added.
AQAP has claimed responsibility for the failed December 25 attack on a Northwest Airlines plane.
Washington has confirmed the Al-Qaeda franchise in Yemen was behind the attack and said that it trained the alleged Nigerian assailant, Umar Farouk Abdulmutallab.
Yemeni officials also announced last week the capture of Mohammed al-Hanq and two other militants believed to be behind threats against Western interests in Sanaa that caused embassies to close for several days.
Yemen is under US pressure to clamp down on Al-Qaeda, and analysts say that the government in the impoverished state is keen to show the world it can crush Al-Qaeda militants on its own.
Yemen "wants to avoid a foreign military intervention targeting Al-Qaeda," said Adel al-Ahmadi, a Yemeni specialist on the group.
"Yemen is trying to say that it can accomplish the mission on its own, and just needs logistical assistance... and political support to consolidate its regime in the face of local adversaries."
For Sanaa, the "successive and successful strikes carried out since December 17 prove that logistical and intelligence assistance is more effective" than direct intervention by foreign forces, said analyst Said Ali Obeid al-Jamhi.
The council of Yemeni clerics warned on Thursday of jihad, or holy war, if there is any foreign military intervention in the country.
An international conference on Yemen will be held in London on January 27.
"It's our duty to help Yemen," Kuwait's Foreign Minister Sheikh Mohammad al-Sabah told Al-Qabas newspaper in an interview to be published on Sunday.
"They (Al-Qaeda) are trying to convert Yemen into a centre for the export of international terrorism and we must confront them."
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