What to reply a PhD supervisor who says my chances of getting selected in this scholarship program are not very high?

The professor is saying no. He is being polite about it, but he's saying he doesn't want you in his group. Arguing with him is not going to change that. (In fact it's more likely to solidify in his mind that you are a bad candidate, with poor social skills, who would be a poor fit in his program.)

Look for somewhere else to go.

I agree with iayork that your professor appears to be giving you a polite and implicit "no", framed in a way that requires you to read-between-the-lines. However, he hasn't been explicit, and if you want to follow-up to get an explicit answer, you should feel free to do so.

If this is indeed a read-between-the-lines-no, then further inquiry into the matter will probably just get you a more explicit "no". However, you could reasonably make your inquiry tangentially, by asking this professor for some advice on what additional work you would need to do to become a competitive candidate, and get to a level where he would support your application. From his email, clearly one thing you can do is to publish some academic work; you could reasonably ask if there is anything else you ought to be doing to become competitive.

You reply: "Thank you".

It's rare that a professor will be so direct and tell someone outright not to try to apply for a given program/scholarship because they don't stand a chance. I don't know SINGA but scholarship applications usually require a lot of work on your end (and also from other people, like the ones writing recommendation letters). This professor is doing you a favor by telling you your time and efforts would be most likely better invested in something else. For example: becoming a stronger candidate, alternatively apply to a less-competitive scholarship.

Don't take it personally. There are many reasons that make some people eligible and most others not.