In one case, footage of an octopus scrambling out of a tank and hopping overboard was obtained by pouring bleach in the tank, the newspaper said, reporting on a BBC documentary on Cousteau to be broadcast next week.
For the filmed story of two sea lions that were caught and trained to walk on the deck of Cousteau's research vessel Calypso before returning to the sea, the crew actually used four sea lions because the first two died during filming, the newspaper said.
"We kept them out of the sea too long to make the film," Calypso crewman Albert Falco was quoted as saying.
The Cousteau Foundation has denied such accusations in the past but was not available for comment Sunday.
Diving team member Andre Laban said he once was told to pretend to have symptoms of the "bends," or narcosis, a dangerous ailment caused by sudden changes in pressure when divers return to the surface.
"There were a lot of things which were not as truthful as they might have been," he was quoted as saying.
In "The Silent World," which won an Academy Award for best documentary in 1957, Laban was told to spend three hours in a decompression chamber because Cousteau was worried he had the ailment.