The 4-year-old polar bear died Saturday afternoon in front of visitors.
Polar bears usually live 15 to 20 years in the wild, and even longer in captivity, and the zoo is hoping the investigation may help clarify what happened.
Results were expected later Monday or on Tuesday, the zoo said.
In the meantime, people continued to flock to the zoo to sign their name in a condolence book in tribute to Knut.
Knut was rejected by his mother at birth, along with his twin brother, who only survived a couple of days. He attracted attention when his main caregiver, Thomas Doerflein, camped out at the zoo to give the button-eyed cub his bottle every two hours. The bear went on to appear on magazine covers, in a film and on mountains of merchandise.
Doerflein, the zookeeper who raised him, died in 2008.
Soon after Knut and Doerflein's first public appearance in early 2007, fan clubs sprang up across the globe. "Knutmania" led to a 2007 Vanity Fair cover with actor Leonardo DiCaprio shot by photographer Annie Leibovitz, a film and plush Knut toys.
Zoo spokeswoman Claudia Beinek said that they had to set up another condolence book online to accommodate the outpouring of sympathy from around the world for the polar bear.
In addition, the zoo said it was starting a special account to accept donations on Knut's behalf, which will be used for polar bear research and the preservation of their habitat.
"He has brought joy to us, the Berliners and many others around the world," the zoo said in a statement. "Knut also was an icon for the endangerment of his species and natural habitats of all wild animals."
Online condolence book: