Malaysian tax is territorial scope.  The fact your company is not in Malaysia and doesn't have a branch in Malaysia is one factor.  You need to consider the following:-

- 1)When you are employed, are you working in Malaysia (i.e. representative of your company in Malaysia)

If your answer is "yes" then your income is taxable in Malaysia notwithstanding your income was not paid by a Malaysian company (this is because you have exercised employment in Malaysia).
- How long were you in this employ?

There are specific rules that grant tax exemptions depending on how long you were in their employ.  (if more than 182 days, forget about this point).
- What country is your company based in?

This can also lead to tax exemptions depending on the country  (if more than 182 days employment, forget about this point).