California's effort to stop the rapidly spreading Mediterranean fruit fly failed for the third time this morning to meet its aerial spraying schedule and prompted a U.S. Agriculture Department official to complain of the slow pace.

"We're not happy about it, simply because the spraying is not getting done," said King Lovinger, spokesman for the department's animal and plant health inspection service in Washington, D.C. Agriculture Secretary John R. Block has threatened and vegetables, half the nation's production, if the rapidly breeding fly is not stopped.

A spokesman for the Los Gatos headquarters of the effort to eradicate what is commonly called the "Medfly" said only two of the five helicopters available were able to fly early this morning. Their spraying covered only 18 square miles, bringing the total sprayed to 25 square miles. More than 140 square miles are infested with the flies.

Lovinger said the 140-mile-square-mile infested area could have been covered "in three days" with proper equipment. He acknowledged that the state officials have been plagued by mechanical failures in the helicopters, thickened pesticide mix jamming the pumps, fog, confusion among the ground crews, and the need to calm area residents who fear health hazards from the presticide malathion.

In the wake of Gov. Edmund G. (Jerry) Brown Jr's request Wednesday for federal disaster relief for the three San Francisco bay area counties involved, California's office of emergency services prepared information today for the Federal Emergency Management Agency on how much additional federal money was needed to help the aerial and ground spraying and tree stripping program.

Brown said the local quarantine barring shipments of any fruits and vegetables from San Mateo, Santa Clara and Alameda counties had already caused $4.2 million in losses by local farms and businesses. But the three counties around the south end of San Francisco by have become heavily residential in recent decades. Their total fruit and vegetable production is about $93 million in a state that produces $14 billion in agricultural products each year.

What concerns state and federal agriculture officials is the threat that the fly and its larvae, which feed under the skin of fruits and vegetables and spoil them for market, could reach the San Joaquin Valley, one of the most important growing areas in the country.

State officials quickly organized an expanded aerial spraying schedule for the city of Milpitas when new Medfly larvae were found there Tuesday. The city at the southern tip of the bay is only about 30 miles across the Diablo Mountains from the San Joaquin. New larvae also appeared Wednesday in San Mateo, a 10-mile jump from the northern limits of the aerial spraying program. State officials said they expected they would move the spraying further north, but were much more concerned about the flies in Milpitas.

Medfly project spokesman Gene Cone said two Hiller helicopters brought in by a new contractor, Evergreen Helicopter Service, had "hydraulic problems in the spraying equipment" and could not fly this morning. A third Evergreen helicopter had a "valve problem," she said.

Evergreen has been linked by news reports in the past with the Central Intelligence Agency. Although the company denies ties with the CIA, it bought one of its subsidiaries from the agency in 1975. An Evergreen jet flew the late shah of Iran from Panama to Egypt during his exile.

The original project contractor, San Joaquin Helicopter Service of Delano, Calif., managed to get both its helicopters in the air this morning after waiting four hours to see if federal rules barred flying in low fog. It had managed to get only one machine in the air each of the first two nights of spraying.

Officials have limited aerial spraying from midnight to 6 a.m. to lessen exposure by residents of the thickly populated area, even though state and federal officials deny any health hazard from the spray.

The helicopters covered only a square mile Tuesday, six square miles Wednesday and about 18 square miles this morning, leaving them far behind the 45 square miles they were scheduled to have covered by this time. Project spokesman said they still hoped to have about seven helicopters available by the weekend, however, and expected the problems with the spray devices would be solved.

One official said the mixture of pesticide, which kills the insect by causing respiratory failure, and syrup to attract the fly was too thick in some cases to flow smoothy from the long spraying device carried under the helicopter. The mixture has been made thicker than usual to ensure that its falls in droplets rather than in a mist that might be inhaled by residents. Each droplet is about the size of the period at the end of this sentence. The spray delivers about two droplets per square foot.

California has spent about $22 million on the Medfly project and the federal government about $3.2 million. Brown said the fly could not be controlled without more federal money in a letter to President Reagan Wednesday. Federal officials said today they were still studying and seeking more information about the state's request.

State agricultural official Gordon Snow and federal spokesman Lovinger both discounted earlier reports that the new Medfly outbreak might have been caused by an ongoing program to unleash sterile flies to upset the Medfly life cycle.