The Metro board, seeking to end a 12-year battle, yesterday endorsed a controversial plan to construct a section of the Green Line through Northwest and Northeast Washington, including a subway tunnel beneath historic Rock Creek Cemetery.

"We have been a very, very long time coming to this decision," said Gladys W. Mack, chairman of the Metro board and general assistant to D.C. Mayor Marion Barry. She termed it "the last major alignment decision within the Metro rail system."

The board's unanimous vote was aimed at settling one of the last major disputes that have blocked construction of the Green Line, the only unopened line in the planned Metro system.

The long-debated subway section, expected to cost $444 million, would extend from a proposed Columbia Heights station at 14th and Irving streets NW to the Fort Totten stop in Northeast. Tunnels would be excavated primarily beneath New Hampshire Avenue NW.

The board's vote also was praised by Prince George's County officials, who have long expressed concern that D.C. disputes might jeopardize plans to extend the Green Line to a county terminus at Greenbelt. The newly adopted route "is the right alignment," said Robert B. Ostrom, a county member of the Metro board.

The decision was immediately denounced, however, by neighborhood activists. "We are strongly against it. We always have been against it," said Benjamin L. Spaulding, a longtime opponent of Metro's plans. "There's no benefit for anyone in my area."

Neighborhood leaders have contended that excavation of subway tunnels would cause disruption, including noise and possible damage to homes, in Petworth and other moderate-income communities. In addition, they have argued, the route would benefit suburban commuters rather than Petworth residents.

The board of governors of Rock Creek Cemetery also has opposed the route, saying that subway tunnels would mar the 18th century burial site, listed in the National Register of Historic Places. Under Metro's plans, a tunnel, described as 34 to 100 feet deep, would be excavated beneath a 2,600-foot section of the cemetery.

Ernest F. Henry, the cemetery board's general counsel, said yesterday that the board will consider challenging the Metro proposal in court. In a letter, the cemetery board said it is "unalterably opposed" to the plan and "will resist by every means at our disposal any attempt to invade the cemetery by tunnelling or any other method."

Prospects for building the 2.5-mile section of the Green Line are uncertain because no federal funds have been set aside for the project. Nevertheless, Metro's plans call for opening the section in 1996.

The battle over the route began at hearings in 1973 when an earlier proposal was assailed by what Metro officials have described as a "barrage of criticism" from neighborhood residents. The initial plan provided for tunnels beneath Kansas Avenue NW. Since then, the route has undergone extensive study.

Metro officials said they shifted to the New Hampshire Avenue route partly because it was found to cost less than other proposals. It also appeared likely to attract relatively high ridership, cause comparatively little community disruption and allow for smoother train operations, they argued.

They disputed claims by neighborhood activists and by the cemetery's board, saying that the project would have "minimal impact" on the area. Mack said the District will offer "special consideration" to residents displaced because of construction. The plan is expected to affect 98 homes.

Other disputes that delayed the Green Line's construction recently have been settled. Work has started on a section in Anacostia, which had been held up by a court challenge. The board ended a conflict in Prince George's by choosing a southern terminus near Branch Avenue. Efforts are under way to resolve conflicts near South Dakota Avenue NE and in College Park.

However, several new disputes, including claims of inadequate participation in construction work by minority-owned businesses, have raised possibilities of further delays.

Yesterday, the Metro board voted to reject all bids for constructing an $11 million parking garage at the proposed Anacostia station after civil rights officials found the lowest bidder failed to meet minority-contracting goals. An investigation has begun into similar allegations over bids for building the proposed Shaw station in Northwest. The company has disputed the claims.