Pension adjustment to taxable pay.

I have an employee making personal pension contributions which are allowable as a reduction against her taxable salary. If I put the amount in as a Pension - RAC deduction it does deduct the amount from her gross salary and calculate the correct PAYE however it also applies it as deduction from her gross salary this is not correct as she is making the payment from her personal funds. Anyone know how to treat this situation? Thanks.