The steps the council would follow to ensure a fair and measured process was carried out and costings would be decided over the next few weeks, he said.
"The fact that these complaints go back a number of years now make it more challenging, but it's our belief that they do need to be revisited to the best that we are able."
Wintec has declined to release details of the complaints and allegations relating to Flowers, citing confidentiality and privacy.
The chief executive, senior management and staff had been informed of the developments and Flowers remained in the top role with the support of the Wintec Council.
"I've spoken to senior management and they remain supportive of their chief executive and focused on delivering on the organisation's objectives."
Review of Wintec investigation into CEO looks at whether council needs to reopen investigation
The launch of a new investigation has been welcomed by a former Wintec staffer who took part in the first investigation and believed everyone would be happy to take part again.
The woman, who did not want to be named, believed it was a more conducive environment now than when the first investigation was carried out in 2015.
In November last year, Harris defended the original investigation to the Herald, saying the allegations were looked into independently and were unsubstantiated.
He made the comments after the Herald revealed Wintec had spent almost $175,000 fighting a media organisation publishing stories about it and its staff, including its chief executive.
The costly legal advice was also used to help deflect defamatory allegations and statements from disaffected third parties about Wintec and its staff with no evidence supplied, he said at the time.
Meanwhile Audit New Zealand is continuing its audit of Wintec which includes scrutinising expenses incurred by the chief executive and his executive team between 2009 and 2017 in relation to travel to Hong Kong and China.
The work, estimated to cost $80,000, is expected to be completed in either June or July.
Review of Wintec investigation into CEO looks at whether council needs to reopen investigation
Wintec to launch independent peer review into complaint relating to CEO Mark Flowers