Australian defense officials announced the death but did not state the cause.
Warren, whose father was killed in a plane crash in 1934 in Australia, was a research scientist at the Aeronautical Research Laboratories in Melbourne.
He came up with the idea of a crash-proof and fireproof machine to record the crew's voices and instrument readings after helping investigate the mysterious crash of a Comet commercial jetliner in India in 1953.
In 1956 Warren designed and built the first flight data recorder prototype, which became known as the black box, but it took five years before the value and practicality of his invention was realized.
Initially the Royal Australian Air Force said that "such a device is not required.... The recorder would yield more expletives than explanations."
It took several more years until authorities ruled that the flight data recorders should be standard equipment fitted to all cockpits.
"The modern-day equivalent of Dr. Warren's device, installed in passenger airlines around the world, is a testament to his pioneering work," said a statement from the Australian Department of Defense.
"It is now also used in other forms of road transport to capture information in the lead-up to accidents. Dr. Warren's flight data recorder has made an invaluable contribution to safety in world aviation."
Warren was born in 1925 on an island off the northern coast of Australia, the son of a missionary. He attended boarding schools in Sydney and later studied chemistry at the University of Sydney.
In 2002, Warren was appointed an Officer in the General Division of the Order of Australia, one of the nation's highest civilian honors. In 2008 Australia's national carrier, Qantas, named an Airbus A380 aircraft in his honor.
Survivors include his wife, four children and grandchildren.