From recent experience (this month):

going between cebu and negros oriental by ferry - may or may not need proof of vaccination. A copy of my EU vaccination certificate was sufficient, if the coast guard was actually checking for it. Last two times nobody asked. Some form of ID (passport always works) should be with you anyways.

Dumaguete - Siquijor
Need hotel booking confirmation and proof of vaccination. Again, EU vaccination certificate was no problem.

Siquijor- Dumaguete: nobody asked.


So someone vaccinated flying in to Cebu or Dumaguete could do these places without any problems. That is of course just now and may change anytime …