Professional tax is a state levy, and the state that matters is the one where the employee works — not the one where your company is registered.
This sounds obvious stated plainly. It is also the single most common multi-location payroll error, and it is invisible until you have a second location.
Why it stays hidden
A single-location company cannot get this wrong. The head office state and the workplace state are the same state, so any system produces the right answer regardless of which one it reads.
Open a second branch and the two diverge. If your payroll resolves PT from the company's registered address, it now deducts the head-office slab from everybody — and it will keep doing so, quietly, correctly-looking, for years.
What follows from it
Registration in each state where PT applies. One registration does not cover employees working elsewhere, and remittance is state-specific.
Different deductions for identical salaries. Two employees on the same pay in Maharashtra and Karnataka will have different PT. That is correct, and it is worth explaining to them before they compare payslips.
Transfers change the deduction. An employee moving between branches moves between slabs, from the effective date of the transfer. If your system holds placement as a dated assignment rather than as a field that gets overwritten, this happens by itself.
Some states do not levy it at all. So the correct deduction for a branch in one of them is nil, not the head office amount.
The remote-work question is genuinely unsettled
Where an employee works permanently from a state in which you have no establishment, practice varies and the position is not uniform across states. If you have a meaningful number of people in that situation, it is worth taking local advice rather than defaulting to the office state because it is easier.
What to check this month
Run a list of employees by workplace state alongside the PT deducted for each. If every employee shows the same slab and you operate in more than one state, you have found it.
It is a small monthly amount per person, which is exactly why it goes unnoticed — and why the accumulated shortfall across a few years of a growing branch is larger than anybody expects.