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Section E is usually used for child care vouchers or luncheon vouchers.
If you reimbursed your employee directly in cash or through the payroll for his private fuel, that would be subject to employee Class1 NIC through the next payroll. If he had the use of a company credit card, then Class 1A NIC is due on the private fuel costs which should be shown in Section M, box 151A of the P11D. See Section 11 and Appendix 1 of CWG5 here.
I hope this helps but let me know if you have any further questions.
The benefit to the employee is the VAT inclusive figure so that is what goes in the first box. The "Amount made good" box is what the employee pays back to the employer, if anything, to reduce the taxable benefit.