The federal Urban Mass Transportation Administration has upheld a move by the Metro system to reject the lowest bid on a contract to construct a subway station for the Green Line in Washington's low-income Shaw area and instead award the $50.9 million project to the second-lowest bidder.

Metro officials turned down the lowest bid in June, citing violations of minority-business requirements. The dispute is among the latest in a series of conflicts that have delayed construction of the Green Line, the only unopened route in the planned 103-mile subway system.

Nevertheless, work on the Shaw project is expected to remain stalled until a federal judge rules on the issue. Yesterday, Judge Louis F. Oberdorfer scheduled a U.S. District Court hearing for next Friday and said he would seek to issue a ruling by Aug. 24, the current expiration date for the bids.

The Shaw station, at Seventh Street NW between R and S streets, is scheduled to open in 1990. Metro officials have warned that any court order barring work on the station might further delay the Green Line.

In a ruling made public yesterday, UMTA rebuffed a protest filed by the rejected bidder. Peter N. Stowell, administrator of the agency's Mid-Atlantic region, held that the Metro system had "a rational basis" for turning down the lowest bid.

The authority had rejected a $49.4 million bid from a joint venture formed by S.A. Healy Co. of McCook, Ill., and Vanessa General Builders Inc., a black-owned company based in Bridgeview, Ill. Vanessa has been the focus of allegations labeling the firm a "sham" and a front for white-owned businesses.

After an investigation, Metro officials concluded that Healy and Vanessa had shown "a lack of good faith" to comply with minority-business rules, which require 20 percent of the work to be carried out by black-owned or other "disadvantaged" firms. The companies have denied the allegations.

The Metro board voted to award the contract to a joint venture consisting of Mergentime Corp. of Flemington, N.J., and Perini Corp. of Framingham, Mass. Officials said those companies have complied with minority-business rules.

In another development, Metro officials expressed concern over a deficit-reduction plan adopted by Congress Thursday night. The plan includes an overall 15 percent cutback in most transit programs.

Officials said the cuts may result in a loss of $37.5 million in federal aid for Metro subway construction next year, along with sizable reductions in outlays for buying buses and subsidizing deficits. But Congress may modify the proposed spending levels in future appropriations measures, officials said.