I do not think there is enough information in the original post. Tax liability on Company Cars is based on their emissions and initial full list price, not the purchase price. The tax liability is also increased if fuel is provided for private use, which includes travel to and from the place of employment. The tax liability is considered to be the tax on the financial benefit of the car to its user, which is deducted from the Tax Free Allowance. So if a Car and fuel is considered to be worth £5,000.00, then tax needs to be paid on that, so the Tax Free Allowance will be reduced by £5,000.00, a reduction of Tax Code by 500. Depending on the car, the Tax code can actually end up negative, which used to be indicated by a K by the tax code. So a 100k code would mean you pay tax as if you had no Tax Free allowance, and were earning £1000.00 on top of that. I can assure you it can become punitive if you are a higher rate tax payer!
I must admit I thought a P46 was submitted if an employee did not have a P45, and as such would not relate to Company Car benefit. I think at the end of the tax year the Company should submit a form (P60) detailing income and tax and NICs deducted and a P11D to detail all Benefits in Kind, Company Car, Car fuel, telephone, Private Health care etc, at that stage it should trigger HMRC to issue a Self-Assessment form. If the wrong amount of tax has been paid HMRC will either issue a refund or a demand, depending if tax has been over or under paid. The tax payer may then be given the option of receiving or paying in a lump sum, or having the tax repaid or recouped in the next tax year via a Tax Code change. Eventually it should all come out in the wash, but there may be some peaks on the way.
For certain a Company Car is no longer the beneficial perquisite it used to be. It will be worthwhile recalculating if a Company Car is beneficial, or if a car allowance plus mileage is better, even if you provide your own car.