An ambulance spokeswoman said emergency services were called to the elephant enclosure and discovered that a woman in her 40s had been injured.
"She had critical injuries, multiple injuries. The patient was unconscious and had stopped breathing," the spokeswoman told.
She was resuscitated and taken to a nearby hospital.
The zoo said the woman was conducting a routine training session when "a young male elephant pinned the female keeper against a bollard".
"Two other keepers in an adjoining stall responded to her call and moved the elephant away," it said, adding that the public was never at risk.
"An investigation has been immediately commenced into this incident and what may have prompted the reaction.
"It's unknown at this time why the young elephant challenged the keeper," the zoo said.
A herd of Asian elephants was brought to Australia from Thailand in 2006 in a bid to increase numbers of the endangered animals and Taronga Zoo now has eight in captivity.
Male Asian elephants can weigh more than five tonnes and be more than three metres (nine feet) tall.
Friday's incident is not the first animal attack at the zoo, which is on the banks of Sydney Harbour and a popular attraction for tourists.
In 2010, an 11-year-old boy was mauled by a sea lion during a show after being chosen from the audience to get up close to the creatures.