How to get from either Negros or Cebu to El Nido in Palawan?
It seems there are no direct flights.
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There aren't many flights to El Nido from anywhere, never mind from Cebu or Negros. There used to be a SEAir flight which I've taken and which was a wonderful experience, taking off from the giant NAIA at Manila in a tiny plane and coming in to land just a few metres above the sea :) You can still fly there on ITI - but I think resort customers may get priority.
WikiTravel has info on transport to El Nido. Don't think that the lack of flights shown is due to the page being incomplete - El Nido airfield is just that, a field, and it doesn't see much traffic.
To cut a long story short, you'll need to get yourself to Manila and take a (prebooked) flight with ITI or any other small airline which may now fly there, or get to Puerto Princesa and go up to El Nido in one of the regular vans.
Ferry may also be an option from Manila to PP, if you're a bit of a masochist.
If money is tight, fly Cebu to Puerto and then overland. If money no option, fly to Manila and then to El Nido but do check the flight to El Nido is running and has a seat beforehand!
(EDIT: ITI website claim the airstrip has been upgraded but so far as I know none of the usual suspects fly there yet - Air Asia, PAL, Cebu Pacific, etc.)
The only flights to El Nido are by Island Transvoyager (ITI). If you are staying at one of the pricey all-inclusive resorts operated by El Nido Resorts (Lagen Island, Miniloc Island, Apulit Island, Pangulasian Island) you can coordinate with the resort to book your flight via ITI. The airline is under the same parent company as the resorts. They don't appear to have an active website, and don't seem eager to attract non-resort business.
An indirect but much more reasonably priced option would be to take a flight to Puerto Princesa (direct flights from Manila, Cebu and Iloilo on Cebu Pacific or Philippine Airlines). From there you can book a tourist van for a 6-hour ride to El Nido. An air conditioned tourist van is much more comfortable than the open buses that locals would take. In my opinion, a good deal.
It's a long trip but El Nido really is beautiful and worth the trip.