Cricket Australia (CA) announced on Wednesday that Lee would miss the three-match series for personal reasons, and newspaper reports on Thursday said it was because his two-year marriage to Liz Kemp was over.
The 31-year-old Lee will also miss the pre-series training camp in Coolum.
The pair married in June 2006 in a lavish ceremony, after Lee proposed to the podiatrist on a tour of South Africa.
Their son, Preston, was born later that year.
The Daily Telegraph said the relationship had been on the rocks for a couple of months, the news breaking just days after the fast bowler launched his own brand of men's underwear.
"Brett needs time to work through things," a close friend of Lee was quoted as saying. "Obviously, it's a tough time for him."
Lee's management refused to comment on the claims.
In a surprise move, Lee was replaced for the three-match series by Tasmanian Brett Geeves, who has not previously played for Australia.
Australia were already without captain Ricky Ponting for the series, while he recovers from wrist surgery. Opener Matthew Hayden has been named for the series, despite lingering concerns over an Achilles injury.
All three matches will be played in Darwin, on August 30, and September 3 and 6.
The series is currently scheduled to be followed by the troubled Champions Trophy in Pakistan. Australia then have a Test tour of India, where Lee is a massive star, having recorded a hit Bollywood single last year.
Lee is soon to make his Bollywood film debut in Victory, directed by Manmohan Shetty.