The capture of Mohammed al-Lahji, the Al-Qaeda chief in the city's Tawahi district, along with two of his bodyguards sparked a gunfight overnight in which a policeman was wounded, they said.
The government imposed a night-time curfew in Aden for one month after clashes on Sunday blamed on jihadists killed at least 22 people, including 10 members of the security forces.
An official at the Aden governor's office said that "homes in Tawahi and Mualla districts are being searched one by one to hunt down terrorists."
Pro-government forces trained by a Saudi-led coalition supporting President Abedrabbo Mansour Hadi set up checkpoints across the city, they added.
Sunday's clashes erupted when forces loyal to Hadi came up against resistance while trying to secure the Aden port, security sources said.
Pro-Hadi forces eventually managed to take control of the facility after hours of fighting.
Aden, declared by the government to be the temporary capital, has seen a growing jihadist presence with Al-Qaeda in the Arabian Peninsula, long active in Yemen, and the Islamic State group apparently vying for influence.
"We will work on forcing the armed groups out of government buildings. We will cleanse all neighbourhoods from terrorists" Aden police chief General Shallal Ali Shayae told reporters late yesterday.
The city was rocked by months of fighting last year between pro-government forces and Iran-backed Shiite Huthi rebels who seized the capital Sanaa in September 2014 before expanding south.
Loyalists have regained control of Aden and four other southern provinces since July, but the rebels still hold Sanaa and have besieged the third city of Taez for months.
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