Australian says divers were injured after the Chinese navy used sonar while they were in the water clearing fishing nets.
Australia's defence minister Richard Marles said the government had expressed his concerns to Beijing for its "unsafe and unprofessional" use of the technology. It comes after similar complaints from the US, Canada and Australia over alleged actions taken by Chinese forces in the western Pacific.
Mr Marles said the HMAS Toowoomba stopped while it was in international waters on Tuesday in Japan's exclusive economic zone after the fishing nets became caught on its propellers.
It had been helping the UN enforce sanctions in the region.
He said: "While diving operations were under way, a PLA-N destroyer (DDG-139) operating in the vicinity closed towards HMAS Toowoomba.
"Toowoomba again advised the PLA-N destroyer that diving operations were being conducted and requested the ship keep clear.
"Despite acknowledging Toowoomba's communications, the Chinese vessel approached at a closer range. Soon after, it was detected operating its hull-mounted sonar in a manner that posed a risk to the safety of the Australian divers who were forced to exit the water.
"The divers sustained minor injuries, likely due to being subjected to the sonar pulses from the Chinese destroyer."
Sonar uses sound waves to get an image of what is happening in the water.
When used at high levels, it can cause dizziness and in some cases organ damage.
Opposition politician James Paterson said the incident happened after the prime minister visited China to build closer ties.
"On one hand, China says it wants a better relationship with Australia and on the other hand it takes dangerous manoeuvres that put the safety of Australian personnel at risk," he told reporters.
China did not immediately respond to the accusations.