Adm Harry Harris, speaking in Beijing, said such moves should surprise no-one.
An unnamed US official earlier told Reuters similar patrols would take place at least "twice a quarter".
The guided-missile destroyer USS Lassen breached the 12-nautical mile zone that China claims around the Subi and Mischief reefs in the Spratly archipelago.
Admiral Harris, of the US Pacific Command, said in a speech at Peking University: "We`ve been conducting freedom of navigation operations all over the world for decades, so no-one should be surprised by them."
"Our military will continue to fly, sail, and operate whenever and wherever international law allows. The South China Sea is not - and will not - be an exception."
But he also added that the operations, which he described as "routine", should "never be construed as a threat to any nation".
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