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ABC News reports the plane, Flight 1716, landed safely, but the 62 passengers on board were evacuated on the tarmac.
Sources told Action News that a piece of baggage dropped off a cart, and a clerk got nervous after hearing a bang.
About 22 bags were cleared in Philadelphia, but one bag on the departing flight needed to be checked.
Once the flight landed in Boston, the bomb squad checked, then cleared, the bag in question.
ABC News also reports that the bomb squad was called, but has cleared the scene.
In a statement, U.S. Airways said "Our first priority is the safety of our passengers and we are working closely with Boston airport and law enforcement authorities on this situation. All passengers have safely deplaned and have been moved to a building near the terminal at this time."
Meanwhile, the Associated Press reports that United Airways Flight 636 to Chicago was returned to the gate at Logan and passengers sent back through security screening at the request of the crew while the aircraft was swept on Tuesday. A United spokeswoman did not say why.
Security has been at a high alert since Monday's bombings at the Boston Marathon that left three people dead and more than 170 others injured.
There is no word on who set off those bombs or why.