During both a TS 16949 Gap Analysis by our registrar and also during our registrars AS9100 surveillance audit the issue of qualification and competence of both internal auditors and the auditor trainer were questioned. I had the suspicion early on that this question would become an issue once ISO 19011 was issued and I was right.
The best way to handle this would be to develop a list of internal auditor qualification requirements. We developed them from ISO/AS/TS standards requirements for auditors, guidance/requirements found in ISO 19011, IAF and IATF Rule 2, internal audit procedure and customer requirements. Your auditors should then be evaluated during either mock or real audit just like the big boys do during RAB auditor certification.
This evaluation must be conducted by a qualified individual, i.e. one who has attended an RAB-accredited internal auditor or lead auditor course. This worked for us and our registrar was happy.
One final note we just had DoD and Two aerospace primes audit us and they also asked for the same.