U.S. District Court Judge June Green refused late yesterday to stop implementation today of a new subway and bus-fare schedule for the entire Metro system.

The 11th-hour request for an injunction came from a group of D.C. City Council members and citizens including Council member Marion Barry (D-at-large) and Sammie Abbott, a long-time opponent of freeways in the District.

The court's action means that Metro's 10-cent increase to 50 cents for rush-hour bus fares and its new automated subway fare scheduled were to go into effect as scheduled this morning at the same time Metro's new 12-mile subway line starts operations.

Landon G. Dowdey, attorney for the plaintiffs, said he would appeal Judge Green's ruling in U.S. Court of Appeals today.

The action by the court was the second last-minute procedural matter that had to be resolved before transit operations could begin today, the first day of Metro's new fiscal year.

The other matter was cleared after a lengthy Metro Board meeting yesterday morning when board members finally agreed to authorize general manager Theodore Lutz to sign a transit services agreement with Fairfax County.

That agreement provides that Metro will give bus and subway service to Fairfax County residents in exchange for money. The money, a three-month payment to be advanced today, is necessary for the system to operate.

Fairfax County had added a provision to the agreement that said, in effect, that it would not pay beyond the three months unless everybody else paid. "Everybody else" is a euphemism for Falls Church and Fairfax City, which for different reasons have disputed the amount of money they owe the Metro system.

The board wrangled for almost two hours, including a 25-minute caucus, before approving the contract Fairfax County had forwarded with a covering letter stipulating that the contract would be renegotiated within 90 days or would not be valid, in effect the same thing the contract already said.

The amount of money involved is $529,800, or six-tenths of 1 per cent of Metro's total estimated operations deficit for fiscal year 1978.

The request for an injunction was lodged first as a petition to the Metro board late in the day, then as a formal court complaint. The fare structure was adopted by the Metro board May 19.

The structure was adopted unanimously by board members including both of its District of Columbia representatives - alternative directors Jerry A. Moore Jr., an at-large Republican member of the City Council, and Douglas Schneider, director of the D.C. Department of Transportation who sits for Mayor Walter Washington.

At the time of the board action, Council member Barry was seeking full City Council support for retention of the 40-cent city bus fare at all times. His resolution never got out of committee, although it had been mailed to all Council members.

Joining Barry and Abbott on the petition yesterday were Council members David A. Clarke (D-One), Willie J. Hardy (D-Seven), Hilda Mason (S-at-large), Douglas E. Moore (D-at-large). Wilhelmina Rolark (D-Eight), Polly Shackleton (D-Three), and John A. Wilson (D-One).

Judge Green wondered out loud why the petitioners had taken so long to challenge the fares before the court.

In an interview last night, Dowdey said he had been out of town and had started working on the matter only in the last two weeks.

Dowdey charged that the Metro Board had not adopted the fare structure it had taken to public hearing and that Schneider was not eligible to represent the mayor.