The shootout late on Saturday in the Borneo town of Semporna followed a firefight Friday between Filipino followers of a self-claimed sultan and Malaysian security forces, which left 12 intruders and two police officers dead.
The five deaths in Semporna – 300 kilometres (190 miles) from the site of the three-week standoff – came after police were "ambushed" by gunmen during a security sweep, Malaysia's national police chief Ismail Omar told reporters.
It was not immediately clear whether any of the alleged Semporna gunmen had suffered casualties.
An estimated 100-300 Filipinos have been surrounded in a farming village by a Malaysian police and military cordon since landing by boat from the nearby Philippines to insist the area belongs to their Islamic leader.
The leader, Jamalul Kiram III, 74, claims to be the heir to the Islamic sultanate of Sulu, which once controlled parts of the southern Philippines and the Malaysian state of Sabah on Borneo.
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