"Make no mistake, the United States will fly, sail and operate wherever international law allows, as we do around the world, and the South China Sea will not be an exception," Carter told a joint news conference.
"We will do that in the time and places of our choosing," Carter added.
He had been asked about reports that the United States had already decided to conduct freedom-of-navigation operations inside 12 nautical mile limits that China claims around islands built on reefs in the Spratly archipelago.
The Boston meeting brought together Carter, U.S. Secretary of State John Kerry, Australian Foreign Minister Julie Bishop and Australian Defense Minister Marise Payne for regular talks between the two countries.
A joint statement said they "expressed strong concerns over recent Chinese land reclamation and construction activity in the South China Sea. It called on "all claimant states to halt land reclamation, construction, and militarization."
Bishop welcomed a statement by Chinese President Xi Jingping last month that China did not intend to militarize the islands and said she hoped Beijing would stick to the commitment.
China claims most of the South China Sea and last week its foreign ministry warned that Beijing would not stand for violations of its territorial waters in the name of freedom of navigation.
Some analysts in Washington believe the decision has been taken and the patrols could take place later this week or next.
"You know, doing the 12 nautical mile challenge is one among a variety of options that we`re considering," a U.S. official said. "We`re waiting for an interagency decision that includes the White House."
The United States says that under international law building up artificial islands on previously submerged reefs does not entitle a country to claim a territorial limit and that it is vital to maintain freedom of navigation in a sea through which more than $5 trillion of world trade passes every year.
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