It is important that the church determine the proper amounts to be claimed for the CPP calculation.  When submitting CPP deductions to the CRA, the church is also responsible to submit an equal amount (ie: for every $100 of CPP deducted from salary, the church is also required to submit $100 to the CRA for the employees CPP).  

Amounts deducted and remitted in error for an employee’s portion of CPP will be refunded back to the employee when they submit their personal tax return.  The church, however, can receive a refund of the employer’s portion of CPP overpayment only if they are aware of it and will have to apply to CRA to receive it.  It can be a difficult and timely process