The attack took place off Yemen's southern coast, the defence ministry said. He was arrested in 2003, but escaped from a high-security prison in 2006.
He was charged with killing a military officer in August 2004. Last week, another Al Qaeda leader, Jumaan Sufian surrendered in al-Jouf province, the ministry said.
The Al Qaeda network in Yemen carried out a series of attacks on security facilities and western targets over the past two months in the country, killing dozens of people.
Yemen is the ancestral home of Al Qaeda chief Osama bin Laden.
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