The men were ordered to run, walk and crawl across contaminated areas but the MoD says they were only exposed to very low levels of radiation and were not put at risk.
British researcher Sue Rabbit Roff discovered a document in the Australian National Archive which revealed that Australian personnel were used to test different types of clothing to find out what protection they offered against radiation.
"We never used people as human guinea pigs," an MoD spokesman said.
"We did conduct tests in the 1950s and 1960s on Commonwealth officers and they were asked to participate as logistical support.
"We were testing the effects of very low level radiation fallout on clothing not personnel."
Ms Roff, senior research fellow at Dundee University, said the document she discovered lists 24 Australian personnel who were used in experiments to see what clothing would be more protective in a nuclear war.
The men were asked to wear particular types of clothing and to crawl and walk through ground zero some hours and days after the detonation of nuclear and atomic weapons at Maralinga," she said.
The Australian Government has said it intends to investigate the allegations.
Nuclear tests timeline
1952-63 - British Government carries out nuclear tests in Australia
1956 - Maralinga becomes location for all tests in Australia
1967 - Maralinga officially closed
1984 Australian Royal Commission set up in response to safety concerns
Britain conducted a series of tests at Monte Bello Island off Western Australia and at Maralinga in the southern Australian desert.
Morris May, a lawyer representing a group of 30 Australian veterans seeking compensation for exposure to radiation during nuclear testing, told the radio his clients had long claimed they were used as guinea pigs.
He said one veteran, a driver, had described how he had been instructed to walk through a contaminated area wearing army issue woollen clothing. No one believed him.