The Boeing 777 plane carrying 233 passengers and 15 crew members took off from Tokyo's Haneda airport at 11:00 am (0200 GMT) but returned to land an hour later.
Footage shown by public broadcaster NHK showed the plane safely landing at the airport.
"It seems that a bird got sucked into the left engine when taking off," a JAL spokesman told AFP.
"The plane discarded fuel in the air" to reduce weight ahead of landing, he said.
"We closed this runway as there may be some parts that dropped from the plane," he said.
There was no immediate information on any damage sustained by the plane or injuries to the passengers or crew and no major delays were caused by the incident.
Haneda -- officially known as Tokyo International Airport -- is the world's fifth busiest airport, according to Airports Council International, with more than 75 million passengers each year.
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