China has been trying to build deeper ties with ASEAN, but tempers have flared during territorial spats over disputed territory in the South China Sea.
China claims most of the entire sea on historical grounds, but Vietnam, the Philippines, Brunei, Malaysia and Taiwan all strongly disagree. A number of maritime incidents between China and its neighbors has increased tensions in recent years, raising concerns about potential violence.
"We should abandon a Cold War mentality and advocate common security and collaborative security," Xi said.
"For the territorial and maritime disputes between China and ASEAN, the two sides should adhere to the principle of peaceful consultation and frank dialogue and resolve these disputes in a peaceful manner so as to safeguard regional stability and peace," he added.
Xi also met with business leaders during his two-day visit. He is expected to visit Malaysia and attend the Asia-Pacific Economic Cooperation summit next week in Bali.
China is Indonesia's second-largest trading partner. Two-way trade reached $66 billion last year, while Chinese direct investment rose to $2 billion.