Airline flights were delayed as much as two hours in arriving at Washington National Airport yesterday after a Civil Service Commission salary ruling went against the 80 air traffic controllers there.

Five of the airlines serving national reported arrival delays of from 30 to 90 minutes. Passengers told reporters that the delays were as much as two hours.

"I can substantially say we are not having a slowdown," said Harry Hubbard, the chief of the air traffic control tower at National. However, he went on, "I'd have to stay that some of the guys are not extending the second effort."

The Civil Service Commission ruling on a petition by the National controllers seeking to upgrade their Civil Service ranking from Grade 13 to Grade 14, could cost each controller there about $5,000 a year.

No one, including the controllers whose petition for upgrading was denied or responsible Federal Aviation Administration officials, would say how long the flight delays or lack of second effort would continue. Controllers at many other high-traffic airports recently have been promoted from Grade 13 to Grade 14 after a work-to-the-rule nationwide slowdown in July, 1976. The average Grade 13 federal worker gets $28,623 a year: the average Grade 14 gets $33,825 annually.

This situation is apparently confined to National Airport, although a large number of delayed flights from a terminal as important as National sends ripples throughout the East Coast air traffic system.

John Leyden, president of the Professional Air Traffic Controllers Organization (PATCO), said "PATCO is in no way connected with the slowdown" although he expressed his "personal sympathy for the controllers."

Others were not so sympathetic. One man at National Airport, who had delayed on the Eastern Airlines shuttle from New York, pushed away from a reporter in anger and said, "The controllers can stick it."

Another man, Don Rynd, from Long Island, said that on his shuttle flight (delayed 90 minutes in the air). "The pilot came on and said we'd be delayed because of a controllers slowdown. Then he said, if anyone would like to call the tower, here's the number.

Jack Synder, station master for Delta Airlines, said delays of up to 90 minutes were "playing hell with connecting passengers. They're missing flights.

The delays began on Wednesday, according to airline spokesman, but escalated yesterday. A heavy thunder-shower that rolled through the area in midafternoon also caused some flight delays, and bad weather in the Mid-west has added problems.

According to tower chief Hubbard, planes from the Northeast were being held in circling patterns over Baltimore while planes from the West circled west of Dallas International Airport.

Richard E. Swauger, who has been an active PATCO member at National, is the one who filed the petition for upgrading. Such petitions were encouraged by the settlement of the July, 1976, slowdown.

At that time, the Civil Service Commission decided that controllers at high-density airports and regional centers should received the higher-paying Grade 14. Washington National was exclude from the initial settlement.

Swauger filed an appeal in April on behalf of himself and other National controllers. They have always felt that, even though National has fewer flights than such airports as Chicago's O'Hara. Atlanta or New York's Kennedy, the complexity of the control problem here should be a factor in the ratings.

The answer to Swauger's petition, he said, was that Washington national did not handle enough flights to warrant the higher rating.

"It's a numbers game," said Hubbard. "If you, average more than 100 flights per hour in a 16-hour day, controllers get grade 14. We average 97.7. But because of the National curfew (on jet flights between 10 p.m. and 7 a.m.) we have only a 15-hour day of heavy traffic. If our traffic is divided by 15, we average 100.1 flights per hour."

The National Airport tower controls flight not only for National, but also at Andrews Air Force Base and some other small area airports. The control problems are complex, because air traffic has to be worked in around high-density patterns at Dulles and at Baltimore-Washington-International.

National Airport has only one main runway, but is the nation's 10th busiest commercial airport. Most other airports in major centers have two or three parallel runways.

National controllers normally run a tight, closely coordinated operation to get the amount of traffic they handle on and off that single runway. If they relax a little and expand intervals between takeoffs and landings, it is not difficult to delay traffic in the sky and still be following the FAA's rule book.

"Even though they have high traffic counts at Philadelphia, for example," one knowledgeable FAA expert said, "It's a rocking chair operation. Nonetheless, they get Grade 14s. I'm not surprised the National guys are ticked off."

Swauger said that he would appeal the Civil Service Commission ruling.

The top brass at the Federal Aviation Administration was taken by surprise. "We didn't know at the upper levels that this petition had been made," said an FAA spokesman. "The Civil Service Commission asked some lower-level staff for some documents, and they routinely sent them over. I don't know whether we will support the controls' appeal."