Troubled by the prospect of mounting operating deficits from the Metro transit system, the Virginia legislature yesterday called on Metro to enact annual fare increases to keep pace with inflation.

The action by the House of Delegates makes Virginia the first of the three major jurisdictions composing the Metro transit system to proclaim an official policy on how Metro should meet what are predicted to be its sharply rising costs.

Unless the fares for both Metro buses and subways are raised annually, Northern Virginia legislators said yesterday that property taxes in the Washington area would have to be increased to meet the local government's share of Metro's costs.

Althoug the resolution, which had been approved previously by the Senate, does not carry the weight of law and is not binding on the transit system, Del. Mary A. Marshall (D-Arlington) said it should "greatly strenghten our hand" in dealing with Maryland and District of Columbia members of the system.

Virginia transit officials have long urged that Metro recoup more of its operating costs from fares, a position that accounts for the fact that Virginia Metrobus fares tend to be higher than in the District or Maryland.

The resolution, which was directed to the Metro governing board, passed the house on a voice vote and without debate. It had the support of a broad range of Northen Virginia legislators and in the Senate had been supported from the outset by some of that body's most conservative members.

The lack of debate and apparent lack of opposition in the House to Gov. John N. Dalton's plan to spend another $10 million on the Metro subway in the next two years were seen by some legislators as signs that the General Assembly finally has recognized a state obligation toward the region's transit system. Dalton also released this week a $10 million Metro appropriation that his predecessor, Mills . Godwin, had withheld. The House votes on the new $10 million appropriation today.

According to a recent consultant's report. Metro's annual operating deficits will reach' $90 million by 1990 even if fares are increased to match the rate of inflation. If they are increased at half the rate of inflation and the entire 100-mile subway planned for the region is built, the operating deficit could approach $300 million a year, according to the sonsultants.

In a related transportation action, the House yesterday passed and sent to Dalton a Senate bill that will allow Virginia's two Eastern Short counties to continue to divert $95,000 of their secondary road construction funds for operation of a railroad line. Del. Robert S. Bloxom (R-Accomack) said the state's powerful Highway and Transportation Department, which has opposed all diversions of highway funds, agreed to the diversion only as a gap measure to prevent the collapse of rail service on the Eastern Shore. CAPTION: Picture, Virginia Del. Warren Barry (D-Fairfax) holds a check for $10 million, which was released this week from Highway Department funds by Gov. John M. Dalton for Metrorail. Former Gov. Mills Godwin had withheld the Metro appropriation. UPI