The Australian defence minister said a Chinese warship had resorted to "unsafe and unprofessional" actions during the encounter off Japan earlier this week.
The warship approached an Australian frigate as divers were clearing fishing nets from its propellers, he said.
The Chinese ship then emitted dangerous sonar pulses, the minister added.
This had posed "a risk to the safety of the Australian divers, who were forced to exit the water", Defence Minister Richard Marles said in a statement on Saturday.
The divers suffered minor injuries that were likely caused by the sonar, Mr Marles said.
"Australia expects all countries, including China, to operate their militaries in a professional and safe manner," he said.
The Australian long-range frigate HMAS Toowoomba had communicated its intention to conduct diving operations on normal maritime channels, and using internationally recognised signals, the statement said.
There has been no comment from the Chinese government.
According to the Diving Medical Advisory Committee, a London-based body,high levels of underwater sound can cause "dizziness, hearing damage or other injuries"to divers.
The reported incident occurred on Tuesday in Japan's Exclusive Economic Zone. HMAS Toowoomba was conducting operations in support of UN sanctions enforcement, Mr Marles said, without giving details.
Earlier this month Australian Prime Minister Anthony Albanese made abreakthrough trip to China, and hailed "significant progress" in relations between the Pacific powers.
However tensions remain, notably over security. Australian has expressed concern over China's growing assertiveness in the Asia-Pacific region.
Canberra has recently deepened military ties with the US andoverhauled its defence posturein a bid to counter potential threats from China.
Australia has accused China's navy of using sonar pulses in an incident in international waters that resulted in Australian divers suffering injuries.