The motorised vessel carrying seven Britons, two Chinese, one Australian and the three Filipino crew members capsized on Thursday afternoon, according to a statement released by national police headquarters in Manila.
The Boracay tourist police dispatched a boat to the scene and rescued all the foreigners but the three sailors could not be found, the statement said.
The search for the three is continuing, the statement said, without giving a reason for the mishap.
Boracay, a small island with powdery-white sands and clear waters, is one of the Philippines' biggest tourism drawcards.
What the stars mean:
★ Poor ★ ★ Promising ★★★ Good ★★★★ Very good ★★★★★ Exceptional