The FAA stressed that no serious incidents have been linked to problems with the pumps, which are made by Hydro-Aire Inc. of Burbank, Calif., and were installed in January and April on Boeing 737s, 747s and 757s.
The airlines were given four days to inspect their fleets. The FAA estimated 1,250 pumps could have a problem with wires that were placed too close to a rotor and can chafe.
Ron Wojnar, the FAA's deputy director of aircraft certification services, said any airlines with the pumps are being ordered to keep enough fuel in the tanks to cover the devices even when the planes bank or encounter turbulence in flight.
Wojnar said the submersion would prevent any sparks from igniting fuel vapors.
"This is not an unsafe condition," he said.
The order affects 515 of the 737s, 247 of the 747s, and 678 of the 757s operated by U.S. carriers.
Foreign airlines operate about 2,100 of the Boeing jets. The FAA is sending advisories about the pumps to its counterpart agencies in those countries.
The FAA will issue a follow-up directive in a few weeks, instructing carriers to repair or replace any faulty pumps, Wojnar said.
The pumps are located in the center fuel tank under the fuselage. Some planes may also have pumps in wing tanks.
Boeing spokeswoman Liz Veridier said her company sent the airlines a bulletin Wednesday ordering the pumps to be replaced on 116 new planes that had been put into use this year.
Other 737s, 747s and 757s were ordered to fly only with their tanks full enough to cover the pumps until further inspections could be carried out, she said.
The problem was detected on three planes that had pumps short out and stop working, giving the crew an indication of low pressure in the tank, said FAA spokesman Les Dorr.
The British carrier easyJet sent the pump back to Hydro-Aire on Aug. 12 after the crew of one of its Boeing 737s detected low pressure, Dorr said. A week later, a Northwest Airlines 747-400 reported a low pressure indication and found the same problem, he said. A China Southern Airlines 747-400 experienced the same trouble.
The National Transportation Safety Board ruled that an explosion in the center fuel tank of TWA Flight 800 caused it to crash off the coast of Long Island in 1996. It said vapors in the nearly empty tank probably were ignited by a spark in wiring.
The Paris-bound Boeing 747 exploded in a fireball at 13,700 feet, minutes after leaving John F. Kennedy International Airport. All 230 people on board were killed.