The school's board of trustees announced on Friday it had requested Dunedin-based consultant Cleave Hay to prepare an issues report which could be ready by the end of this month.
He has already had contact with some people who have raised concerns.
Mr Hay has had extensive experience in assisting the New Zealand School Trustees' Association and schools and with the Ministry of Education through the intervention process, most recently with Wanaka School.
He has been assisting the Waitaki Boys' trustees in dealing with comments and complaints about management and administration at the school, but not with the process involving a senior staff member.
Another trustees' association representative had been appointed to continue that role so Mr Hay can carry out his independent issues investigation.
Yesterday, after an approach by the Otago Daily Times, Mr Hay outlined the process he would follow, emphasising he acted completely independently.
''The purpose is that I independently investigate the alleged issues at Waitaki Boys' for parents/whanau, staff, ex-staff and then present a report to the board outlining the overarching issues and make recommendations to deal with the areas of concern.''
No names would be recorded or reported unless participants specifically asked for that, and no-one quoted.
Mr Hay said he would meet parties anywhere they wished, including their homes.
The terms of reference from the board involved administration and management, which incorporated issues raised publicly such as bullying, staff turnover and welfare, boarding and public criticism.
Tomorrow, Thursday and Tuesday next week, he will meet people at a venue away from the school to discuss their concerns.
He would also meet the board and senior management, former teachers and would also like to have discussions with former pupils who finished school last year.
Interviews would start with Mr Hay outlining issues to be investigated, how he would go about it, confidentiality and allowing people to determine whether or not to proceed.
After listening, Mr Hay would determine what was relevant and make recommendations in the final report.
From that, he would discuss with the board what action should be taken and offer to act as facilitator to resolve issues.
Mr Hay can be emailed at cleave@staffordbusiness.co.nz