The incident comes amid heightened tension in the South China Sea, in particular over China's land reclamation and over its claims to vast swathes of the resource-rich shipping corridor.
Several Southeast Asian countries have overlapping claims in the area though Indonesia does not, and it sees itself as an "honest broker" in the various territorial disputes.
Indonesia's foreign minister, Retno Marsudi, said she had met Chinese embassy representatives in Jakarta after an incident at the weekend involving the Chinese coastguard vessel, a Chinese fishing vessel and an Indonesian patrol ship in an area known as the Natuna Sea.
"At the meeting we conveyed our strong protest (over) ... the breach by the Chinese coastguard of Indonesia's sovereign rights," Marsudi told a news conference.
Indonesian authorities attempted to detain a Chinese vessel they said was fishing illegally in its waters, an Indonesian official said earlier.
Eight Chinese crew members were detained but the Chinese coastguard prevented Indonesia from securing the fishing vessel.
China has said the fishing vessel was operating in "traditional Chinese fishing grounds" and has demanded the fishermen be released.
"When it comes to fishery disputes, or maritime issues, China is always ready to work with Indonesia to solve these disputes trough negotiations and dialogue," Chinese embassy official Sun Weide told reporters in Jakarta after meeting the Indonesian fisheries minister.
China claims almost the entire South China Sea, a strategic shipping corridor, also rich in fish and natural gas, where several Southeast Asian countries also have overlapping claims.
But China and Indonesia do not contest the sovereignty of the Natuna Islands and the seas around them: both agree they are part of Indonesia's Riau Province.
But tension between the two sides does flare every now and then, usually over Chinese fishing boats.
In March 2013, armed Chinese vessels confronted an Indonesian fisheries patrol boat and demanded the release of Chinese fishermen who had been apprehended in Natuna waters. Fearing for his safety, the captain of the Indonesian boat complied.
Similarly, in 2010, a Chinese maritime enforcement vessel compelled an Indonesian patrol boat to release another illegal Chinese trawler.
Indonesia has no plans to boost military resources in the remote, resource-rich Natuna Islands in response to the latest incident, the defense minister said.