It is understood the legendary British performer considered canceling his Australian tour but decided to soldier on after meeting with tour promoters.
"They have been having a great time since they arrived last week but David suddenly took ill and has flown back to Los Angeles for specialist treatment," a source told The Daily Telegraph.
"David had various appointments and engagements set up during the tour but he's had to cancel them. Elton was obviously extremely distressed, and his first instinct was to leave the tour to be with his partner when he was ill.
"But he spoke to his old friend Michael Chugg who is promoting the tour, and in the end they decided the tour -- the show -- should go on."
John and Furnish married in a civil ceremony in the UK in 2005, and had brought their young son Zachary out to Australia for a tour which began in Sydney last week and moves to the northern New South Wales region of the Hunter Valley this weekend.
It was not known if Zachary flew home with Furnish or remains on tour with John. Details of Furnish's condition were unclear.