Is this correct? - A housing allowance of eg. 50,000 was provided. The ACCOMMODATION cost eg. 62,000 and the company paid the full amount therefore the employee owes the employer 12,000.
While many companies will deduct it over the entire year eg. 12,000/12=1,000pm I do not believe they are required to do so by law as it is my understanding that the deduction of advances/allowances do not fall under the gamut of the labour law areas as it is seen, as madolecow said, as a benefit.
I would check your HR policies, contract and anything you have signed.
For interests sake what is the amount and how much do they want to deduct (%)?