Dear Srinaren,
Usually, the power to collect Professional Tax vests with Local Self-Government institutions (Panchayat, Municipal Corporation, etc.). For each state, there are separate Acts and Rules to govern these institutions. According to the Kerala Panchayat Raj Act Sec 205F and the rules thereunder, Bonus also has to be taken into account for computing the Professional Tax. I find no other reason to include a clause contrary to this in the Act applicable to your area. Hope this will clarify the doubt.
Nasir Ali