Security forces arrested Ali Muhammad Umar Shurbajy in the mountainous Abyan region in south Yemen on Monday night, the Web site of the ruling General People's Congress said on Tuesday. A hunt is still on in the same area for three other wanted men.
Last week eight men, including six suspects in the attack on the US warship, surrendered to the authorities after a week-long siege of armed Islamists in Abyan.
During the operation security forces arrested local al-Qaida leader Abd al-Raouf Nasib, who Yemeni officials say masterminded a 2003 jail break by al-Qaida suspects in the bombing of the ship.
Yemen, the ancestral homeland of Usama bin Ladin, has been battling armed fighters since the 11 September attacks on the US.