Pan American World Airways said yesterday it has filed an application with the Japanese government for permission to operate its three weekly flights from the United States to China via Tokyo.

Under the terms of a bilateral agreement signed in September, Pan Am was selected by the United States to be the first U.S. flag airline to begin regularly scheduled service between the United States and China for the first time since 1949 and was scheduled to begin that service next month.

But Pan Am's new China service has become embroiled in the complicated U.S.-Japan aviation relationship, and its start-up date has already been put off until late January at the request of the state Department.

The U.S.-China bilateral agreement calls for each country to designate one airline to operate between New York, San Francisco, Los Angeles and Honolulu and the Chinese cities of Beijing and Shanghai with an intermediate stop in Japan. The intermediate stop is the immediate problem.

Pan Am and U.S. government sources both say the Japanese government may try to block Pan Am's use of Tokyo as the way station on its new transpacific service. Japan has complained for years that its post-war agreement with the United States favors the United States and its airlines. For instance, the Japanese note that four U.S. airlines are allowed to land in Japan, but only one Japanese carrier, Japan Airlines, can fly to the United States under the agreement.

Pan Am officials say that service to China will be started even if the airline is denied access to Tokyo. Pan Am can fly to China directly from the United States or can stop at other overseas points.

Pan Am's request for stopover rights in Tokyo will be discussed by Japanese and U.S. negotiators in Honolulu beginning Jan. 12 when the two sides come together to try to work out a new aviation agreement acceptable to both sides.

In the meantime, Pan Am has scheduled an inaugural flight for Dec. 6 and has delayed inauguration of its regularly scheduled service until Jan. 28. aIt plans to use a 269-passenger Boeing 747-SP on the China service

In other airline news yesterday, the Civil aeronautics Board:

Recommended to the White House that Air Florida be designated as the second U.S. airline to serve the Miami-London route. Pan Am already flies the route, but flies to Heathrow Airport. Under the terms of the recently-amended U.S.-U.K. bilateral agreement, a second airline could be named, but must use Gatwick Airport. The CAB recommendation must be approved by the president since an international route is involved. World Airways also sought the route.

Recommended to the president that Texas International Airlines be granted authority to fly between Dallas/Ft. Worth and Mexico's Yucatan Peninsula. Braniff Airways was originally granted the route, but asked for a delay in beginning service, causing the CAB to ask if other airlines might like to begin service by mid-January. Besides TI, American Airlines also applied. Washington-area travelers will be able to connect to the new service through TI's non-stop service to Dallas from Baltimore/Washington International Airport.Washington lost its nonstop service to the Yucatan when Evergreen International asked for a delay this fall.

Said that airlines wishing to experiment with their own methods of segregating smokers from nonsmokers during flights may apply for special authority to do so.