Up to 10 members of the MNLF got off their vehicles in Canelar Village near police checkpoint, the Zamboanga City government said in its Twitter.
Two of the rebels were confirmed shot while the rest are being pursued.
It also clarified that aside from Talon-Talon, Santa Barbara, Santa Catalina, Kasanyangan, and Mampang, operations are still ongoing in Canelar as of 3 p.m.
The public was advised to stay calm and vigilant.
The village of Canelar is located less than 2 kilometres from the Zamboanga City international airport and Edwin Andrews Air Base of the Air Force.