Service for imported iPhone
It sounds to me like the store you bought it from, imported it as a grey import from Hong Kong. However, all iPhones come with a global warranty, so you will be covered.
You need to contact Apple directly - someone there will be able to organise something for you. You may need to provide proof of purchase, so have that ready (scan it in if you haven't got a digital copy).
For your info, below is a similar experience I'm aware of firsthand.
I recently helped a lady who purchased a new iPhone from a local online store. About 10 months later the iPhone developed a fault, and while it was definitely under warranty, it took a while to establish this fact because the serial number came up as having been purchased in Thailand, and because it was dated about 7 weeks earlier than when she had purchased it.
In this case, she needed to show her purchase receipt to correct the commencement date for her warranty, as it was originally showing as only 8 days remaining compared to the two months she thought she had left. It did get all sorted, but the issue had to get escalated before it was resolved.
I bought a grey-market iPhone 4S in Thailand that had come from Hong Kong originally. The following year I went to Indianapolis in the US, and on the four flights from Bangkok to Indianapolis, the screen had started to come apart in the top-left corner. Since there is an Apple Store in Indianapolis, I went there and asked if it was possible to get it repaired, and the woman at the store looked up the serial number and told me that it was 11 days inside its warranty. She said come back in the afternoon and she would have a new replacement for me. I told her I needed it to be factory unlocked since the one I bought was factory unlocked, and she said it was not a problem.
I went back in the afternoon, and was given a brand new (seven weeks old! I looked up its serial number online) iPhone with the same spec as the one I had has for nearly a year. With a new battery and everything!
I was extremely impressed with this level of service. We do not have anything like this in Thailand, as the nearest official Apple store is a two-hour flight away in either Hong Kong or more recently Singapore.
If you have a chance to take it to HK or SG (if you know someone going there, for example), I would strongly recommend going to an official Apple store, if you don't have one in the Philippines. The service is astonishingly good - and they don't care which market the phone was designed for, or where it was originally bought.