I had exact issue. It's common knowledge that you will get engine check light if you remove catalytic converter or your O2 sensor has carbon/residuals on it. Even though car works fine otherwise. If you notice the dashboards of other vitz on road or signals, almost 50% of them has engine check light.
In my case, it was a malfunctioning fuel injector. Once replaced (Kabli/1000rs) the light came back only once or twice for few seconds, which also resolved after replacing a corroded harness/grip. Don't worry about engine check light, it usually means to have your car checked soon. It may just be asking a regular maintenance like replacing spark plugs or clogged cat-convertor.
I heard a rumour that Pakistan is shifting to better quality fuel from Nov-2016, may be someone would confirm if it's true.
( Personally I have started to dislike JDM cars, good quality build but have lots of engine and cvt problems/ batteries reaching end-of-life or tempered odometers. Way too many variables to worry about.)