Dear Bhavi,
I am not sure I understand (i) the problem (ii) the need to introduce "Non Taxable" Allowances to increase the take home and (iii) the reason for the difference of Rs 4,000/= plus between CTC and take home.
You mention that the monthly CTC is Rs 13,000. This works out to an Annual CTC of Rs 1,56,000/= which is below the taxable bracket. There would not be any Income Tax deduction taking place for such employees. Since no tax is deductible, introduction of "Tax Exempt" allowances will not make any difference.
An Illustrative Salary Stack could be worked as follows (I am mentioning tax deductible amounts, even though in the case that you have cited, no Tax is payable becuase the annual income is below the Tax threshold.):
Basic Rs 5,200/= per month or Rs 62,400 per annum
HRA Rs 2,080/= per month or Rs 24,960/= per annum (Since Vadodara is a non metro location only 40% of basic is eligible for a Tax deduction, which is computed as the minimum of three computations.)
Transport Allowance Rs 800/= per month or Rs 9,600/= per annum. (This is a tax exempt allowance to the extent of Rs 9,600 per annum)
Special Allowance Rs 3,670/= per month or Rs 44,040 per annum. (This is salary paid which does not count towards PF)
Medical Reimbursement Rs 1,250/= per month or Rs 15,000 per annum. (This is amount is exempt from tax against submission of bills)
Aggregate Rs 13,000/= per month or Rs 1,56,000/= per annum.
Provident Fund deduction (taken at 8.33%) is Rs 433/= per month or Rs 5,196/= per annum.
Since no tax is deductible, the Net Salary Payable to the employee would be Rs 13,000/= less Rs 433/= i.e., Rs 12,567/= per month or Rs 1,50,804/= per annum. This is 96.67% of the CTC.
While this gives an alternative, I still haven't been able to understand the three issues that I mentioned in the beginning of the post.
I hope this response is of help to you.
Regards
Raju Bhatnagar