I think there is some confusion between "Medical allowance" & "medical reimbursement".
Under the head salary, all the sum to be received/receivable by the employee is essentially part of the salary, unless it is excluded by some other provision.
There is no exclusion for medical allowance and it is always taxable.
Medical reimbursement is not included in the perquisites uptil 15,000. [For more details see below]
It is the responsibility of the employer to provide the details of the amount sort as deduction or exemption. In the absence of the documentary evidence, the actions of the employer were justified.
ONLY following expenses are allowed u/s80D (AND NO OTHER EXPENSE CAN BE CLAIMED U/ SAID SECTION)
(a) the whole of the amount paid to effect or to keep in force an insurance on the health of the assessee or his family or any contribution made to the Central Government Health Scheme or such other scheme as may be notified by the Central Government in this behalf or any payment made on account of preventive health check-up of the assessee or his family as does not exceed in the aggregate twenty-five thousand rupees; and*
(b) the whole of the amount paid to effect or to keep in force an insurance on the health of the parent or parents of the assessee or any payment made on account of preventive health check-up of the parent or parents of the assessee as does not exceed in the aggregate twenty-five thousand rupees;
(c) the whole of the amount paid on account of medical expenditure incurred on the health of the assessee or any member of his family as does not exceed in the aggregate 27[thirty]thousand rupees; and
(d) the whole of the amount paid on account of medical expenditure incurred on the health of any parent of the assessee, as does not exceed in the aggregate 27[thirty] thousand rupees:
However, I would advise you to claim the deduction while filing the return.
From now on, we have back the concept of standard deduction wherein the submission of such documents would not be required. If you have the proof of deduction then it may be claimed. Go for it.
17. For the purposes of sections 15 and 16 and of this section,—
(2) "perquisite" includes—
Provided that nothing in this clause shall apply to,—
(v) any sum paid by the employer in respect of any expenditure actually incurred by the employee on his medical treatment or treatment of any member of his family other than the treatment referred to in clauses (i) and (ii); so, however, that such sum does not exceed fifteen thousand rupees in the previous year;