If you were covered under payment of wages act, the answer would be simple. Maximum deduction from gross salary including PF ESI etc is 50%. So full deduction is not allowed. Further, deduction of excess paid allowances is like a debt recovery so it should come under the other restrictions in the act.
However, I suspect you earn more than ₹18000 per month so the act will not apply to you.
You need to read the standing orders applicable to the state you work and see the rules that apply in such a situation.
The question then comes is why the allowance was paid to you. It must have been in the salary slip so you were aware of it. You can't say you didn't know. If the allowance was paid by mistake they should discuss the same and recover it in instalments. However, if the allowance was paid due to a misstatement, manipulation or fraud by you, then they are pretty much justified in recovery in a single instalment.
First step for you should be to go and speak to th HR and to your immediate manager and complain of how unfair it is to recover in a single instalment. But now it's done, what resolution exactly are you expecting ?