"We have been caught by surprise as to how quickly our situation has become public. It is with regret that I confirm today's media reports are correct and that Liz and I have decided to separate," Lee said in a statement.
"Given the personal nature of the matter I ask that you please respect our privacy as we attempt to deal with this sensitive situation," Lee said.
According to reports, the glamour fast bowler, who had Tuesday become the latest sports star to launch his own line of men's underwear range here, was spending time with his parents and working out his next move.
Lee, 31, and podiatrist wife Liz Kemp, 31, have separated after just two years together. They have a son Preston.
Confirming that Lee had been granted short-term leave, acting Cricket Australia chief executive Michael Brown said: "We look forward to Brett Lee rejoining the group as soon as possible."
Meanwhile, fans of the Australian cricketing legend can look forward to soon seeing him in action on the big screen.
Lee is starring in "Victory", a Bollywood film on cricket to be produced by Vivek Aggarwal and Ajit Pal for Victory Films India, scheduled for release soon.