Western Australia's Environment Minister, Judy Edwards, says she is not convinced by assurances that a series of test explosions off the state's coast will be conducted in line with environmental guidelines.
Geoscience Australia wants to detonate 20 underwater bombs in deep water off Exmouth to assess the agency's ability to detect secret nuclear testing overseas.
Dr Edwards says she first heard about the experiment in a newspaper article.
She is concerned the blasts may endanger migrating humpback whales and the sensitive Ningaloo reef area.
"The proposal is in Commonwealth waters so technically they don't have to tell us but given the closeness of this proposal to the Ningaloo reef and the high values we put both on the Ningaloo reef and on whales who migrate through the area we as a community really need to know about potential environmental impacts," Dr Edwards said.
"At the sites shown to us the coastal shelf is quite narrow and it's quite near the reef."
Geoscience Australia says the blasts will not proceed unless they meet environmental standards.
But Dr Edwards says the Commonwealth does not have a good record on such issues and wants the experiment to comply with WA's own conservation standards.