Milham said he went through the long ERA process to hold the organisation accountable.
"By not - and this is my principle, my integrity - by not challenging it you are enabling the behaviour of senior managers to continue as per the number of confidential settlements you see.
"If they are confidential - there's a reason for it and that's Wintec do not want information put out."
The number of confidential settlements by Wintec was revealed in a response to an Official Information Act request by the Herald. The amount paid out was not specified.
Wintec Council chairman Barry Harris has defended the organisation and said he was surprised by a call for a ministerial inquiry from a former Wintec HR staff member, saying it had no basis.
He had not been contacted by the Education Minister, but was keeping the Tertiary Education Commission informed.
Harris said Wintec had learnt from the ERA findings and he was satisfied by the changes management had made.
The changes included reviewing and updating four policies, better differentiating its investigation process and disciplinary process, providing training to managers and human resources staff about the new policies and running a two-day course for human resources staff around investigations into complaints.
Confidential settlements were made for employment issues rather than entering legal proceedings and he did not think an average of five confidential agreements a year amid some restructures was "out of the norm".
They covered a wide range of matters including performance, misconduct, dismissal, staff complaints and restructuring.
Former Hamilton Labour MP Sue Moroney, who raised concerns around employment issues with the chief executive earlier in the year, believed 45 confidential settlements was an alarming figure for an organisation which should be a model employer in Hamilton.
"Having dealt with the issues surrounding the Ministry of Transport fraud and misspending of taxpayer money at the Waikato DHB, I'm becoming increasingly concerned about the effect of confidential employment settlements on public disclosure of information the public has the right to know about.
"I'm concerned it is increasingly being used as a way of keeping bad behaviour covered up."
Chen Palmer principal of employment Anthony Russell said an average of five confidential settlements a year seemed more akin for an organisation of 4000 to 5000 employees rather than Wintec's 950 staff. However, it would depend on whether there had been several restructures over that time.
"It's up there, but it's not hugely out of proportion I wouldn't have thought. It depends on the circumstances - if they've undertaken a number of restructurings, it could have easily led to a number of settlement agreements - it would depend on what they were for to a certain degree."
Russell said settlements were not unusual and generally ranged in value between one and six months' salary, and no more than $30,000-$40,000 in compensation.