Navy Chief Abdul Aziz Jaafar said that since late 2014, intrusions by Chinese ships into Malaysian waters have been a daily affair with Kuala Lumpur protesting to Beijing each time.
Abdul Aziz told AFP the Chinese vessel involved in the latest incident remained in Malaysian waters.
"We are maintaining our presence there. We are shadowing the vessel continuously. It is a case where they want to maintain their presence there but at the same time we are there to make sure and tell them that this is our waters," he said.
"We have been submitting (diplomatic protests). Every time we detect them... every time we sight them we challenge them (to indicate) that they are in our waters. At the same time we lodge a diplomatic protest," he added.
The latest incident is near the Luconia Shoals, an area of the South China Sea just outside the Spratlys, a reputedly oil-rich island chain claimed in whole or in part by Brunei, China, Malaysia, the Philippines, Taiwan and Vietnam.
Abdul Aziz said the Chinese incursion had taken place very close to the Malaysian coast.
Luconia Shoals lies just 65 nautical miles (120 kilometres) north west of the oil-rich town of Miri in eastern Sarawak state.
Abdul Aziz said in the latest incident attempts to communicate with the Chinese vessel to state that it was in Malaysian waters met no response.
"We are on Channel 16. We are communicating through VHF communications. We are telling them this is our waters. (But) they do not respond," he said.
Beijing, which claims the South China Sea almost entirely, has built 2,000 acres (800 hectares) of artificial islands in the Spratlys, including those with facilities that appear to have a military purpose.