In March, Indonesia attempted to detain a Chinese trawler it accused of fishing in its exclusive economic zone in the South China Sea (Vietnam's East Sea), prompting the Chinese coastguard to intervene.
China has said its vessels were operating in "traditional fishing grounds".
Indonesia is not embroiled in the rival claims with China over the South China Sea (Vietnam's East Sea) and has instead seen itself as an "honest broker" in disputes between China and the Philippines, Malaysia and Brunei.
Meeting on the sidelines of a regional defence ministers meeting in Lao capital Vientiane, Chinese Defence Minister Chang Wanquan said he hoped China and Indonesia would "deepen pragmatic exchanges and cooperation" and promote military ties, the official Xinhua news agency reported on Friday.
"Being two large developing countries in Asia, China and Indonesia have aligned development strategies and broad prospects for cooperation," the report paraphrased Chang as telling Indonesian Defence Minister Ryamizard Ryacudu.
Chang also "made clear China's consistent stance" on the South China Sea (Vietnam's East Sea) issue, Xinhua added, without elaborating.
China's increasingly assertive military posture in the South China Sea (Vietnam's East Sea), a strategic shipping corridor that is also rich in fish and natural gas, has rattled the United States and its allies in Southeast Asia.
China claims almost all of the energy-rich South China Sea (Vietnam's East Sea), through which more than $5 trillion of trade passes each year. The Philippines, Brunei, Vietnam, Malaysia and Taiwan have overlapping claims.