The former X Factor judge, 40, revealed her "sadness" over the break-up of her four-year romance with the 33-year-old English model in a Twitter post.
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Dannii said the couple still cared for each other but their number one priority was now their 21-month-old son, Ethan.
She wrote on the social networking website: "It brings me great sadness to tell you that Kris & I have separated.
"We still care for each other & ask for privacy at this difficult time, in particular for our son Ethan who remains our number one priority."
Meanwhile, former rugby league star Kris also took to Twitter to confirm the split.
He wrote: "Dannii and I have a deep mutual love and respect for each other and although things have not worked out we have a gorgeous son together that we both love and implore everyone to respect our privacy at this challenging time."
Australian singer Dannii, who has also been a judge on Australia's Got Talent, began dating Kris in 2008 after they met in a nightclub in Ibiza.
The couple had shared a home in the suburbs of Melbourne, Australia, after moving from their base in the UK to bring up their young son.