The 2000 Sydney Olympics hero and model Lindy, who married in 2006, earlier blamed hectic work schedules on why they were spending more time apart.
A representative for the couple issued a formal statement saying they had decided to part because it was in the best interests of their three children, Stella, 10, Rocco, 7, and Frankie, 4.
“Michael and Lindy’s children will always remain their highest priority, and their happiness will be Michael and Lindy’s primary focus,” reads the statement.
“We ask that you respect their privacy at this time.”
A report says Lindy, 37, is currently at the family’s home in Bali with her children, having spent time on the New South Wales north coast with friends earlier in February.
At the time the marriage rift rumours first surfaced in 2015, Lindy admitted she sometimes felt guilty about the constant travel she did for her fashion line.
“Sometimes I think, maybe it would be good if I didn’t have to get on a plane all the time and I could have that white-picket-fence life, but I am not that conventional person … the life I live right now suits me,” she said.
Michael, 38, countered by saying they’d been living separate lives for the last three years.
“I can understand how people get the idea that we’ve separated. Lindy’s got her agenda with fashion and we travel a lot. We spend a fair bit of time apart and just because of that, our work commitments and our lifestyle, it looks strange to people.”
Another report says they were last seen out together in early December 2015 at a croquet event in Melbourne.
While Lindy and the children are back in Bali, Michael is understood to have returned to Melbourne.
The couple has built a global skincare business together, Milk & Co, which they launched in 2008.