DEFENCE is investigating claims up to 50 US prisoners died in underground bunkers in secret chemical warfare tests on a coral atoll on the Great Barrier Reef off north Queensland.

The latest probe comes after the discovery of a tunnel under Castle Hill in Townsville this week unearthed an Aladdin's cave of other military mysteries reportedly kept secret from the public.

These include unconfirmed tales of an intact downed Japanese Zero fighter plane on Cape York, secret air bases, buried aircraft, and an underground military hospital.

But military historians allege the biggest untold wartime secret is the unverified death toll - deemed highly classified - in mustard gas bombing tests on Brook Island, 30km off Cardwell, nearly 70 years ago.

Today the idyllic Brook Island group, fringed by coral reef, is a restricted national park and home to up to 30,000 pied imperial pigeons that migrate down from Papua New Guinea every year.

But, in three bombing tests in World War II, it was the top-secret site of a series of Japanese-style underground bunker systems and, according to witness reports, untold casualties of war.

Agent Orange was tested at nearby Innisfail at the start of the Vietnam War - heightening fears of increased cancer links - in "secret tests" revealed in hidden archives in 2008 by researcher Jean Williams, who won an Order of Australia Medal for her study.

Renowned amateur war historians Peter Dunn, of ozatwar.com, and Sid Beck, owner of Queensland's biggest private military collection in Mareeba, claim the truth is yet to be told about the WWII chemical warfare tests.

They cite the eyewitness account of Innisfail-based chemical warfare unit scientist Sylvia Stolz, who took samples of the devastating effects of mustard gas after each bombing sortie on Brook Island in 1944.