Small whales and dolphins are being driven to strand themselves by bursts of ship sonar that sound to them like hunting orca, says a US researcher who is visiting New Zealand.
Dr Christopher Clark said false orca sounds from military sonar could panic whales and dolphins and send them shooting to the surface to avoid attack.
The phenomenon affected small whales, such as beaked whales, but does not appear to panic their larger relatives.
Dr Clark, the director of the bioacoustics research programme at the Cornell Laboratory of Ornithology and senior scientist in the department of neurobiology and behaviour at Cornell University in New York, said panicked whales and dolphins might speed off and beach themselves when they reached the surface in a hurry and found the "orca" sounds had followed them.
Although New Zealand waters were quiet compared with the noisy waters around the United States, too little was known about local species, such as Hectors and Maui dolphins, to guess what effect sonar and shipping noise might be having.
Dr Clark spent almost 10 years getting a whale's-ear view of the sea using high-quality US Navy listening equipment.
He found low-frequency ship sonar would sound like "big daddy humpbacks" to whales, and mid-frequency sonar would sound like orcas.
Dr Clark, who was in Auckland this week to speak about ocean noise, wants more research into whales and dolphins so shipping and naval training exercises can avoid sensitive breeding and feeding grounds.
Like human divers, whales and dolphins can suffer decompression sickness when they rise to the surface too quickly.
British scientists reported evidence of the bends in beached whales and dolphins five years ago.
But they suggested the animals were dying after being startled by deafening sonar booms from military submarine training.
Dr Clark's research suggests that, for some animals, it may be the similarity between sonar and orca calls and not the volume that is the problem.
New Zealand's waters are home to rare Hectors and Maui dolphins, bottlenose dolphins and orca, as well as sperm whales, endangered Gray's beaked whales and Southern Right whales.