The rules surrounding deductions from pay are very clear. You can only take deductions from salary if you either have a clear written term allowing this or you have prior written agreement from your employee before the deduction is made.
Check you company car policy. Do you have a term regarding repayment to the company in the event of damage due to the employee’s actions? What are the circumstances under which you are allowed to make such a recovery and how is the amount to be determined? If there is nothing in the company car policy then you need to look to see if you have a general term in their contract about deductions from pay for costs incurred as a result of his actions.
How has he managed to damage the car though neglect? You will need to demonstrate that he knew what was needed to look after the car but chose not to do so. You cannot charge him for general wear and tear.
If you do not have a contractual term or prior written agreement allowing you to make this deduction then you are not entitled to make it. In those circumstances you need to speak to the employee in question and give him the option in respect of repayment. If he will not agree to repay the money willingly then you will need to explain to him that you will have to consider pursuing the matter through county court. In the event of that happening then you will seek to recover the full costs of the repairs plus any court costs and legal fees.