Gov. Hirokazu Nakaima said Friday approval of the landfill application was given because the application "contains all possible steps that could be taken at present to protect the environment," Kyodo News reported.
"The eagerness exhibited by [Prime Minister Shinzo Abe's] administration is way stronger than past governments," Nakaima said during a news conference in the prefecture's capital of Naha.
He called the latest package presented by Abe "well-balanced."
About 1,000 anti-base protesters stormed the prefecture's government office in Naha after forming a human chain around the building, Kyodo News said. They also called for a meeting with Nakima.
"Okinawa residents cannot tolerate the base relocation within the prefecture," said Akira Oshiro, a 53-year-old worker from Urasoe, who was among the demonstrators.
Since Abe became prime minister a year ago, the central government has amped up pressure on Okinawa to accept construction of a replacement facility in an offshore area in Nago -- as envisioned in 2006 -- to relocate the U.S. Marine Corps' Futenma base from a densely populated area in Ginowan.
The Japanese government had been seeking Nakaima's approval before the mayoral election in Nago next month.
Abe has pledged his government will do "all it can" to limit the issues Okinawa has had hosting the bulk of U.S. military forces in Japan, Kyodo said. Chief Cabinet Secretary Yoshihide Suga said the relocation plan represented the best compromise and welcomed Nakaima's "bold decision."
The Futenma relocation has been an emotional issue in Okinawa, where anti-base sentiment is high amid safety concerns about U.S. military operations.
Calls for the base relocation strengthened after three U.S. servicemen raped an Okinawa school girl in 1995.