Richard Marles said the HMAS Toowoomba -- a long-range frigate -- had been supporting United Nations sanctions enforcement efforts within Japan's exclusive economic zone.
The divers had plunged into the water to clear fishing nets from the ship's propeller, Marles said, when the vessel was approached by a Chinese destroyer.
"Despite acknowledging Toowoomba's communications, the Chinese vessel approached at a closer range," he added in a statement that did not reveal the number of divers involved.
"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 that doctors believed were "likely" linked to the sonar pulses, Marles said.
"This is unsafe and unprofessional conduct," he said.
"Australia expects all countries, including China, to operate their militaries in a professional and safe manner."
China and Australia have been working to patch up their once-close trading relationship after years of bickering and tit-for-tat reprisals.
Australian Prime Minister Anthony Albanese made a breakthrough trip to Beijing earlier this month, hailing the progress as "unquestionably very positive".
But tensions remain when it comes to security, as Australia draws closer to the United States in an effort to blunt China's expanding influence in the Asia-Pacific region.
The Diving Medical Advisory Committee, an independent London-based organisation, has warned that sonar sound waves can cause divers to suffer dizziness, hearing damage and organ damage.
The HMAS Toowoomba -- commissioned in 2005 -- is a long-range frigate packed with advanced surveillance capabilities and "world class" weapons systems, according to the Australian navy.
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