Prabowo's comments, made while he was in Washington on Wednesday, came after his foreign ministry stressed that Indonesia does not recognise China's claims over the South China Sea despite signing a maritime deal with Beijing last weekend.
Beijing has long clashed with Southeast Asian nations over the South China Sea, which it claims almost in its entirety, based on a "nine-dash line" on its maps that cuts into the exclusive economic zones (EEZ) of several countries.
"We respect all powers, but we will always safeguard our sovereignty. But I choose to always find possibilities of a partnership," said Prabowo, who has repeatedly said he will pursue a non-aligned foreign policy.
"Partnerships are better than conflicts," he told reporters.
Prabowo, who is on his first trip since taking office last month, met with Chinese President Xi Jinping in Beijing on the weekend. A maritime development deal signed by China and Indonesia said they had reached common understanding "on joint development in areas of overlapping claims."
That wording sparked concern in Indonesia, with analysts saying it could be interpreted as a change in Jakarta's long-held stance as a non-claimant state in the South China Sea, and risked compromising Indonesia's sovereign rights to exploit resources in its EEZ.
Prabowo did not directly refer to the joint statement in his comments to reporters, but said he had discussed the South China Sea with President Joe Biden in a meeting the day before.
Prabowo will also travel to Peru for the Asia-Pacific Economic Cooperation (APEC) summit and Brazil for the G20 summit.
