Income tax act 40 A (3)

You are right. The section 40A(3) is applicable for income under head PGBP. While the TA/DA allowances provided to an employee comes under 'Salary' head. 

The denial of reimbursement may be due to non providing the valid proof of expense like bill of transporter along with payment receipt by cash; or may be due to any internal advisory for cash payments.

Sec 40( A)3 is a section which embodies lot of aspects.

Cash payment in excess of Rs.20000 is disallowed.

In my case, is it justifiable?

You have right to recover Money. In  many cases particularly in case of Transfer from one city to another city

Person has to attend so many matters . if misses some article in Trasport Vehicle , in majority case he loses it.

Please get receipt of payment from Transport Compnay and claim expenses you have every right to get reimbursement

Sir, if I was not aware about the internal advisory. May I claim the amount?

Yes you can claim 

Now, my department has rejected the bill what can I do now?

Get it reimbursed in your account if possible. 

I could not understand what you mean