Gavin Williamson said the operation would still be going ahead despite the fact Chancellor Philip Hammond's planned meeting with Chinese vice premier Hu Chunhua in Beijing at the weekend was called off.
The Cabinet minister was asked about it at Defence Questions in the Commons on Monday afternoon, with Conservative MP Bill Grant asking "if the Royal Navy will continue with its freedom of navigation operations in the South China Sea."
Mr Williamson replied: "I think, like so many nations such as the United States, Australia, France, New Zealand, Canada - we're all nations that believe in the rule of law and an international rules-based system.
"And we will always be that nation that does not just talk about it, but actually acts to uphold that rule of law that has benefited so many nations, not just ours but many nations right around the globe as well.
"So yes, I do."
The Defence Secretary has been criticised for potentially risking trade talks with China over the deployment of HMS Queen Elizabeth.
He said last week the £6.2 billion ship's first operational mission will be to head to the Mediterranean and the Middle East, as well as the Pacific region, where China holds disputed territorial claims and there is an ongoing row over navigational rights.
Mr Williamson is said to have angered Beijing by saying the UK had to be ready to use "hard power", with former chancellor George Osborne calling it "gunboat diplomacy of a quite old-fashioned kind".
In response, the Prime Minister's official spokesman said:
"In relation to China, I think we have set out areas where we have concerns - such as around cyber-intrusions against the UK and our allies.
"But it is also a country with which we have a strong and constructive relationship."