Contending that a "genuine emergency exists," Braniff International and Pan American World Airways asked the Civil Aeronautics Board late yesterday for immediate reconsideration of their proposal that would transfer Braniff's South American routes to Pan Am for four years in exchange for $30 million.

The airlines told the board that Braniff's South American traffic has fallen off and that it could be in a "negative cash position" as early as Tuesday, with no cash above its domestic needs to help out. "When this happens, Braniff will be forced to shut down its South American operations," they said. Braniff has lost money on the routes for a couple of years, but other carriers say they can make a profit on them.

The board said a week ago that it would make its decision by the end of July after considering the complex competitive issues raised. But it also told Braniff it was willing to consider alternative agreements that Braniff might reach with other airlines for the transfer of its South American routes, arrangements that wouldn't give Pan Am a virtual monopoly there.

Yesterday, however, Braniff said it had talked with other airlines, but that "Pan Am is the only carrier committed to paying Braniff the money Braniff desperately needs" before Braniff's "cash deficit crisis next week . . . and the only carrier ready, willing and able to start service on Braniff's entire South American route system next Wednesday."

The petition, which did not claim that Braniff was close to bankruptcy, was filed late in the day, following the board's receipt of a letter from President Reagan urging it to "take all necessary steps" to ensure that U.S. carrier service continues without interruption on the routes.

The president said foreign policy interests could be "adversely affected" if Braniff were forced to suspend its operations before the board decides and other arrangements were not approved promptly.