US Navy Commander Gary Ross has revealed the Freedom of Navigation Operations (FONOPs) will continue following the pause created by Donald Trump assuming office earlier this year.
China claims about 80 per cent of the South China Sea, including reefs and shoals, but this is disputed by the Philippines, Taiwan, Vietnam Malaysia and Brunei.
Beijing has reclaimed hundreds of acres of land since 2012 to turn seven of these areas into man-made islands with runways and deepwater berths, prompting accusations they are being turned into military outposts.
China could threaten the movement of billions of dollars worth of cargo travelling through the region if Beijing claims sovereignty of the islands.
Under Barack Obama, FONOPs were conducted six times, which usually involved US warships sailing within 12 nautical miles of islets and reefs to test Chinese claims and illustrate they are in international waters.
The pause in operations sparked speculation Mr Trump may have agreed to back off the issue in exchange for Chinese co-operation over North Korea.
Commander Ross told the South China Morning Post: “US forces operate in the Asia-Pacific region on a daily basis, including in the South China Sea.
“We are continuing with regular FONOPs, as we have routinely done in the past and will continue to do in the future.”
He said the controls are “not about any one country” and did not mention China’s claims.
The Pentagon is believed to have turned down requests from US Pacific Command, up until now, to sail warships near Chinese-claimed islands in the region.
This is despite Mr Trump pledging during his presidential campaign to challenge China on constructing military installations on islands claimed by several countries.
Walter Lohman, director of the Asian Studies Centre at Washington DC-based think tank, The Heritage Foundation, said: “It’s fair to say it hasn’t been paused, but it’s also fair to say there have not been any FONOPs since Trump has taken office. We could read too much into that.
“This is a matter of a new administration coming in and having to get its plan together on how to move forward.
“You’re not going to get any more help on North Korea because you are more accommodating to the Chinese somewhere else.
“They have interests in North Korea and those interests aren’t changing.
“If you back off on freedom of navigation in order to get help on Korea what you’re going to end up with is no help on Korea and having ceded your rights on the South China Sea.”