Taxation on Special allowances

Respected Experts my query has not been answered. Kindly help me.

My query :-

As per Sec 10 sub sec 14(I) & (ii) certain special allowances are exempted from tax. The Employer is paying two special allowances as part of Salary as under :-
(1) Special allowance and

(2)Supplimentry allowance

While calculating TDS these two allowances have NOT been deducted from the salary by the persons who are engaged on the job. Kindly clarify whether these allowances are taxable income? Can the Employer give these allowances under a separate head so that tax deduction could be allowed under sec 10. I think the intention of paying these two special allowances separetely by the company is to save tax?