Before crediting salary by the company, that amount of money was not taxed to the company. (if I am right)
After salary is credited to the employee's account that money is subjected to income tax payable by the employee.
In one case when the employee resigned the job the company takes back the previous two months' salary amount from the employee (as notice period penalty deduction) and the employee is also subjected to pay income tax on that deducted two months salary amount.
If it is considered as revenue, and when no expenditure or loss can be shown on it, then that amount of money is subjected to tax payable by company. (if I am right)
In that case the employee also pays tax on the money deducted for him, and the company also pays tax on the same money it received.