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CAMP FOSTER, Okinawa — After a five-month stand-off with protesters at a proposed site for a new U.S. Marine Corps air station, the Japanese Defense Facilities Administration Agency began drilling into the seabed Thursday in preparation for an environmental survey.

Two survey boats and four escort boats arrived at the site off the fishing port of Henoko at about 2:25 p.m. Thursday, drawing surprise from about 200 protesters, part of a group that has maintained a vigil at the port since April 19. The group had prevented survey crews from using Henoko as a base for the survey, which is expected to take six months.

The survey ships returned to the site for 90 minutes Friday morning.

As survey crews set up scaffolding in the shallow waters off Henoko on Thursday to prepare for taking 63 core samples, 16 protesters boarded several small canoes and confronted them.

A Japanese Coast Guard spokesman said the confrontation was peaceful. The protesters, kept at bay by the escort boats manned by local fishermen hired by the DFAA, shouted angrily at the survey crew.

“No major confusion was observed," he said. The coast guard patrolled the area Thursday and Friday.

The survey will establish whether construction of the air station, planned to eventually replace Futenma Marine Corps Air Station, will harm the environment. The air station is to be built on reclaimed land and a coral reef about two miles offshore and is to be connected by a causeway to the Marines’ Camp Schwab.

Opponents say construction will destroy the northernmost feeding grounds of the endangered dugong, a saltwater manatee, and will harm the reef.

A bilateral committee researching ways to consolidate the U.S. military presence on Okinawa decided in 1996 that Futenma, located in the heart of urban Ginowan, should be closed once an alternative location for Marine air operations could be found on the island.

After years of haggling with local politicians opposed to any new military construction, the Henoko site in rural northeast Okinawa was selected.

The base is to be used jointly by civilian aircraft.

“We will continue to proceed with the survey according to a work plan which reflects advice from the Japan Environmental Agency and the environmental concerns pointed out by the Okinawa prefectural government, while giving consideration to the living environment of local residents as well as the natural environment, including the dugongs,” a spokesman for the Naha Bureau of the DFAA said Friday.

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