Prime Minister Yoshihide Suga and his Australian counterpart Scott Morrison on Thursday shared "grave concerns" over China's assertiveness in surrounding waters, Japan's Foreign Ministry said.
The leaders agreed to work closely together to counter China's "unilateral attempts to change the status quo by force" in the East and South China seas, according to the ministry.
During their phone talks, Suga also pointed to Beijing's introduction of a law authorizing its coast guard to use weapons against intruders into its territory as particularly problematic, it said.
Suga also tweeted that they discussed cooperation toward the realization of a free and open Indo-Pacific, collaboration through the Quad, a four-way informal forum of democratic countries also involving the United States and India, and regional issues.
"We, as Special Strategic Partners, will further deepen our cooperation in a wide range of areas such as security and economy," he said.
China asserts sovereignty over the Senkaku Islands, a group of uninhabited islets administrated by Japan in the East China Sea, frequently sending ships nearby to project its power.
China has also continued the militarization of artificial islands in the disputed South China Sea despite an international 2016 ruling against its claims.
During the 40-minute call, the leaders also shared serious concerns regarding the situation in Hong Kong and China's far-western region of Xinjiang, where human rights abuses against the Muslim Uyghur minority have been widely reported, as well as over the military coup in Myanmar, according to the ministry.
The ministry said Morrison praised Japan for its preparations to host this summer's Tokyo Olympics and Paralympics and expressed support for its efforts to secure the return of Japanese citizens abducted by North Korea in the 1970s and 1980s.