Gen Nakatani's visit to the island comes just days before a high-profile trip to Japan by US President Barack Obama.
"I deliver a strong message of regret and at the same time make a protest," Nakatani told US military commander Lt. Gen. Lawrence Nicholson, according to public broadcaster NHK, as he demanded the US military in Okinawa ensure discipline among troops, AFP reported.
Okinawa was the site of a brutal World War II battle but is now considered a strategic linchpin by hosting numerous US military bases.
Police in southern island of Okinawa arrested Kenneth Franklin Shinzato Thursday for allegedly disposing of the woman's body in a weed-covered area in southern Okinawa.
The man, a US citizen and former US Marine, who works at the US Kadena Air Base, has reportedly admitted to killing 20-year-old Rina Shimabukuro, who had been missing since late April.
More than half of the 47,000 US military personnel in the country are stationed in Okinawa, and rapes and other crimes by service personnel have sparked local protests in the past. The heavy US military presence there has long been a periodic thorn in the side of relations.
In 1995 the abduction and rape of a 12-year-old girl by three US servicemen sparked massive protests, prompting Washington to pledge efforts to strengthen troop discipline to prevent such crimes and reduce the US footprint on the island.
But continued crimes by American personnel remain a potent rallying point for Okinawans and others in Japan who oppose the presence of the bases on the crowded island, where pacifist sentiment runs high.