US Navy Vice Adm. Joseph Aucoin's comments come a week after it was revealed that Beijing had deployed surface-to-air missiles on an island in the fiercely contested region.
The US said the presence of missiles provided increasing evidence of militarisation of the area by China.
China subsequently accused the US of militarising the region, saying patrols by US Navy vessels and military aircraft had escalated tensions and raised concerns about stability in the area.
Aucoin, whose Japan-based fleet covers a region from India to the international dateline in the Pacific Ocean, said the US is not making such maneuvers to single out any country, and wants all nations that are reclaiming land to stop.
"I wish it wasn't portrayed as US versus China," Aucoin told reporters in Sydney, one of his stops on a visit to Australia to meet with defence officials.
Last week, US and Taiwanese officials confirmed commercial satellite images showed anti-aircraft missiles had been placed on Woody Island in the Paracel chain. China has not denied the appearance of the missiles, but says it is entitled to defend its territory.
Aucoin said the missiles had provided a "destabilising effect" across the region, and urged China to be transparent about its intentions. Asked whether the presence of the missile system would affect US preparedness to fly over the area, Aucoin said no.
Aucoin also expressed concerns about North Korea's recent nuclear test and rocket launch.
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