Company can issue form no.16 to the employee by stating in it non-deduction of TDS.
But one thing must require to keep in mind in this case:
A Company being an employer may have to suffer penal consequences for non deduction of TDS from taxable salary paid to employee. Penal consequences is summarized below:
a) Charging of interest u/s 201(1A) -
Under Section 201(1A) he is liable to pay simple interest @ 12% per annum on the amount of tax in arrear from the date on which such tax was deductible to the date on which such tax is
actually paid, to the credit of Central Govt.
b) Penalty u/s 221- The assessee in default is liable to imposition
of penalty where the assessing officer is satisfied that the defaulter
has failed to deduct tax as required without good and sufficient
reason. The quantum of penalty is not to exceed the amount of tax
in arrear.
c) Penalty u/s 271C- A penalty equivalent to the amount of tax
the deductor has failed to deduct, is leviable u/s 271C. Such penalty
is however only leviable by a Joint Commissioner of Income Tax.