The victims, 67-year-old Robert Erich Loever and 78-year-old Baltazar Johann Erni, had just stepped out from a beach resort at 1pm (5am GMT) Sunday in Opol town, Misamis Oriental province, when unidentified gunmen shot them in the head, municipal police chief Senior Inspector Alwin Baclao said.
The assailants fled on foot, Baclao said, according to the victims' two female companions who witnessed the attack.
The women were Filipinos and one of them was the girlfriend of Loever, according to local television station ABS-CBN.
Police ruled out robbery as motive after the suspects ran away without taking the victims' belongings, Baclao said, adding an investigation was underway.
Criminal gangs are known to operate in the southern Philippines, prompting China last month to warn its citizens against travel to the area.
The Swiss federal department of foreign affairs has confirmed two tourists died but has declined to comment further.
The Swiss embassy in Manilla is in contact with local authorities.