New York Air faces an important new hurdle on its way to starting low-fare air service Sunday between Washington and New York.

Responding to objections from the Department of Transportation to New York Air's published schedule, NYA yesterday told the DOT it would alter its method of scheduling and selling tickets on two flights each day for which it had not received landing clearance at Washington's National Airport.

The two flights -- originally scheduled to leave New York at 2:30 p.m. and 5:30 p.m. weekdays -- will be scheduled to leave at 2:29 p.m. and 5:29 p.m. respectively and will be considered "extra sections" of the previously scheduled 1:30 p.m. and 4:30 p.m. flights if the DOT approves.

The problem arose when New York Air gained only 18 slots -- permitted landings and takeoffs -- for its National service instead of the 20 it felt were necessary to operate a daily schedule that could compete reasonably with the hourly Eastern Air-Shuttle. Because slots are essentially airline reservations for landings and takeoffs in bad weather conditions -- and there hasn't been a bad-weather day limiting operations at National since mid-summer -- New York Air had scheduled and planned to operate the flights "subject to Air Traffic Control conditions," as its printed schedule says. The caveat meant that the flights would operate except when bad weather caused the airport to enforce stricter flight conditions that bar airlines and private pilots from landing and taking off without slot reservations.

However, the DOT didn't like that idea. Thomas G. Allison, DOT general counsel, said yesterday he told NYA that if the DOT permitted New York Air to schedule flights subject to air traffic control conditions, there would be nothing to keep other major airlines from doing likewise. "We can't break the 40-per-hour rule," he said of the DOT policy limiting the major commercial airlines to 40 slots an hour at National.

The DOT policy, however, specifically exempts extra sections from the 40-an-hour rule, which allows the Eastern shuttle, New York Air's major competitor, to add as many flights throughout the day as it needs to accommodate any waiting passengers at the gate -- without counting against its slot allocations.

"It appears that their proposal revising their operations probably fits the extra-section exemption contained within the high-density rules," Allison said yesterday. But a decision won't be made until today, he said.

New York Air also has run into some trouble with the Civil Aeronautics Board. On Monday, John T. Golden, director of the CAB's Bureau of Consumer Protection, sent NYA a telegram expressing concern about the airline's disclosures to prospective passengers booking the flights. "Although you advertise these flights as 'subject to air traffic control conditions,' you are not telling consumers that these flights may not operate," Golden wrote NYA's president and general manager, Neal Meehan.

Although NYA's proposal to the DOT, if accepted, would mean the likely operation of all the flights, the airline did have a unique backup plan to accommodate passengers in case of flight cancellations: putting them on flights of its major rival, the Eastern shuttle. Lawyers for NYA told the CAB the airline would bus them to the shuttle terminal and pay the difference between NYA's normal daytime fare of $49 and the shuttle fare of $59. The Eastern shuttle routes are the only ones in the country in which a passenger without a ticket who is at the gate by flight time is guaranteed a seat.

Besides the normal weekday fare, New York Air will charge $29 a seat for a lunchtime flight, for a night flight each weekday and for all weekend flights.