Flowers has been on paid sick leave since August.
In a statement released to media today, Flowers said as he was turning 70 next year the timing was right to "hand over the reins".
"I also have current and ongoing health issues," he said.
He was proud of his achievements since he'd been in the role for the past 16 years.
"I have been proud to lead Wintec's international marketing efforts, developing what now
makes up over 20 per cent of Wintec's annual revenue.
"Both my direct involvement, and that of the senior executive, have been critical to this
success, which is particularly important in the Chinese market.
"When I was appointed in 2002, Wintec was under government watch due to poor
financial and academic performance.
"I am very proud to have provided leadership with my team of top managers to establish
Wintec as one of the highest performing institutes in the country."
Wintec chair Barry Harris said although Flowers had given three months' notice as part of his employment conditions, he was not expected to return due to continuing ill health
He doubted there would be outcomes relating to any of the inquiries currently being carried out before Christmas.
"I now don't expect the Wintec Council will be in a position to give an update on outcomes of either of these before Christmas. While this is taking longer than anticipated, ensuring due process is followed and thoroughness of this work is completed, is the important focus."
In an email to staff, Harris said they would celebrate all of Flower's achievement before he officially leaves his post.
"The Wintec Council will look for an opportunity sometime in the New Year to acknowledge Mark's longstanding service and contribution to Wintec's success".
In August, Wintec confirmed Queen's Counsel Simon Mount would relaunch an inquiry into historic allegations regarding Flowers.
The purpose and scope of the inquiry, to begin immediately, is to ensure that:
• The 2015 complaints are fully investigated and conclusions reached on whether the allegations in the complaints have been made out. This excludes allegations relating to spending, which are being separately addressed.
• The report is sufficiently robust for Wintec Council to have confidence in its conclusions;
• Any other relevant matters that come to light are investigated.
