Investigators believe the latest threat was made by a source that may have made similar claims in the past, the bureau said in a statement Tuesday. None of the earlier threats materialized.
The agency said Monday it received a tip from a foreign government source and passed it along to city authorities. Law enforcement responded by bulking up its presence on the Metro.
Extra police and sheriff's deputies, K-9 bomb teams and undercover officers were deployed.
The threat had come from a man and particularly identified the Metro Red Line that stops at Universal City, FBI Field Office Assistant Director Deirdre Fike said Monday.
Authorities said they had briefed reporters because of the specificity of the threat -- and assured commuters that there would be increased patrols and the Metro lines would be safe.
The Los Angeles County Sheriff's Department and Los Angeles Police Department remain on a heightened state of alert, the Tuesday statement said.
On Tuesday, the FBI's Fike thanked law enforcement officers for their swift response -- and the public for its patience.
Earlier in the day, Los Angeles Mayor Eric Garcetti had taken a train from Universal City and reassured people of the line's safety. "One of the lessons from today is all of us can be the eyes and ears on this system and throughout the city," Garcetti said.
There was a visible presence of security from local law enforcement and the US Department of Homeland Security at Union Station, the main hub for the Metro subway, CNN's Casey Wian reported.
"Passenger volume also seemed lighter than normal, and I noticed several passengers as they entered subway cars looking both ways and carefully scrutinizing the car before choosing a seat," Wian said.
The FBI warned that anyone who knowingly provides false threat information to law enforcement is liable for prosecution.