Carter began his visit to Japan on Wednesday as the two allies seek to overhaul US-Japan defense cooperation, according to The Japan Times newspaper.
Speaking at a joint news conference in Tokyo, Nakatani said that moving the US Marine Corps Futenma Air Station to the less populated Nago area was "the sole solution to avoid continuous use of Futenma," the outlet said.
The construction of a new US Marine Corps Air Station in Nago has attracted media attention in recent months amid rallies staged by local environmentalists, who argue that a base would harm flora and fauna in the area and by civic groups, critical of the US military presence in Nago city.
Okinawa Gov. Takeshi Onaga said over the weekend that government perseverance in the face of local opposition has left Okinawans feeling "alienated and angry."
Stiff public opposition has so far prevented the relocation. Apart from environmental concerns, local residents have pointed to a long list of crimes committed by Futenma-based US marines, including several rapes of Japanese schoolgirls and one lethal car accident.