President Joko Widodo also headed Wednesday to the fishing-rich waters around the Natuna Islands, which border the South China Sea, most of which is claimed by China despite competing claims from other Southeast Asian nations including Vietnam, the Philippines and Malaysia.
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The Indonesian military said it had deployed eight warships and four jet fighters ahead of Widodo's visit in an apparent bid to assert its sovereignty over the region.
A Chinese coast guard vessel was spotted near the islands Wednesday, Indonesia said.
"We have deployed eight warships," said Navy spokesperson Fajar Tri Rohadi.
An AFP reporter confirmed with the air force that fighter jets had also been deployed.
It follows the deployment on Friday of around 600 personnel from the navy, army and air force to Natuna as the military launched what it called a regular patrol to secure the area due to the presence of foreign vessels in Indonesian waters.
Jakarta said it would also send hundreds of fishermen to the area to keep an eye out for foreign vessels.
The moves come after Indonesia summoned the Chinese ambassador last week and lodged a "strong protest" over a Chinese coast guard vessel escorting Chinese fishing boats around the islands in mid-December.
Beijing responded that it has "historic rights" in the region and that fishing boats had been carrying out "legal and reasonable" activities.
This week, China's foreign ministry said the dispute was being handled diplomatically.
"China and Indonesia have been communicating on this matter through diplomatic channels," ministry spokesperson Geng Shuang said Tuesday, describing the two countries as "comprehensive strategic partners".
"Both countries shoulder the responsibility of maintaining regional peace and stability," he added.
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Beijing lays claim to huge swathes of the South China Sea, where it is accused of building military installations and artificial islands -- and ramming fishing vessels.
China claims the majority of the resource-rich waterway through the so-called nine-dash line, a vague delineation based on maps from the 1940s as the then Republic of China snapped up islands from Japanese control.
Indonesia does not have a claim in the South China Sea, but said it would not tolerate incursions by China -- a key trading partner -- into its nearby waters.
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