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I suggest to book your flight early,December is a pick season so you may not be able to get a cheap flights.

Air Asia have cheap flights from Melbourne to Philippines.

Well I don't think you'll get cheaper than Malasian Airlines at present....But check-up on your life insurance before you book !!!!

Some examples of Flight prices:
Sydney to Manila flying with CebuPacific (cebupacificair.com) in December 2014. (CebuPacific do not fly to Melbourne)

One Way
A$ 444.25 2nd
A$ 484.25 4th
A$ 594.25 9th
A$ 814.25 16th
A$ 914.25 24th
A$1,014.25 25th
A$ 734.25 30th
A$ 594.25 31st

Taking the date of the 16th as an example, the cheapest I saw on Skyscanner (skyscanner.com.ph) was AirAsia at A$686. A 17 hour flight.

I have looked into visiting philipines in the near future as well. As previously suggested on this thread....malaysian airlines are currently the cheapest and you can get a fare as low as $830 return. Includes a stop somewhere along the way...but no longer than 2hours.
I don't exactly remember how long the total trip will take....I will just estimate it to be between 9-12 hours overall.
If anyone else has suggestions then do tell. As it would help me too.
Fyi some airlines do massive sales. $1 flights or $20 flights are not unheard of. If anyone knows when these sales will take place then give us all a shout
A friend of mine even cashed on one of the sales in phili....flights to Australia for 1Php

I did one of the Cebu Pacific 1 peso flights once, but after fuel surcharge, taxes, fees and booking fees, it came closer to 2,000 pesos   That was for a domestic flight though.

Current Sydney to Manila Return price:

Round Trip
1  Adult(s)  Price Details (AUD)
BASE FARE
(SYD - MNL)
• Adults  106.85 x 1 = 106.85
(MNL - SYD)
• Adults 106.85 x 1 = 106.85
SUBTOTAL : 213.70
WEB ADMIN FEE :  8.00
TAXES AND FEES :  135.15
TOTAL :  AUD  356.85  RETURN  (No More Fuel Surcharges)

BUT:
after it adds baggage allowance and meals the total is AUD 452.85

Dates used:
Sydney to Manila: Departure: 05 March 2015, Thursday
RETURN
Manila to Sydney: Departure: 07 April 2015, Tuesday

What airline or website did you use? That seems pretty reasonable.
If you dont mind posting the website you used to work out that airfare

CebuPacific .
The Australia route is only using Sydney.
cebupacificair.com

I flew with them in November at A$199 one way.  The flight is OK.  Budget price, budget flight