However, New York Police Commissioner Bill Bratton told DNAinfo: "I think it was a significant overreaction."
Ramon Cortines, superintendent of Los Angeles schools who made the decision to close all 900 institutions, told a press conference at 7am Pacific Time he had received an email from overseas describing plans to bomb at least three schools and multiple students.
The threat mentioned backpacks and other objects, he said.
"I can't take a chance, I want all schools to be searched today," Cortines insisted. "I'm not taking a chance of bringing children into a place, into any part of a building, until I know it's safe."
He said he had ordered searches on schools of all kinds - from elementary schools to colleges.
This is not the first threat made against the district but this instance is unique, he said.
However, he insisted he is acting out of "an abundance of caution" in light of the recent attack on the neighboring city of San Bernardino.
Steve Zimmer, president of the school district board, urged: "Parents, if you have not sent your kids to school, do not send them to school."
He said searches would start on all 900 campuses this morning and will be completed within the day. "It's going to be a long day,' he added.
Students who had already arrived at school were sent to specific gates to be collected by parents or guardians.
Parents picking up their children have to bring "proper ID", the school district said.
New York City officials said they received the same threat that led to the closure of the Los Angeles school system but quickly concluded that it was a hoax.
Mayor Bill de Blasio said Tuesday morning that he was 'absolutely convinced' there was no danger to schoolchildren in New York.
New York Police Commissioner William Bratton said he thought Los Angeles officials overreacted by deciding to close the nation's second-largest school system.
He said a school superintendent received the threatening email on Tuesday morning.
Bratton said the person who wrote the note claimed to be a jihadist but made errors that made it clear the person was a prankster.
The closure in Los Angeles could affect tens of thousands of parents who may have to leave work to pick up their children.
Private schools have the option to decide whether or not to close.
All students can ride for free on Los Angeles buses and subways in light of the situation.
Law enforcement teams were seen swarming outside a number of schools, including the Ramon C Cortines Visual and Performing Arts School, which was set up by the superintendent years ago.
A terror expert speaking on CNN surmised that the person or people who made the threat have already achieved most of their objective: instilling terror in the city - and indeed that nation.
"Whoever's put this threat out will be watching this coverage with great satisfaction," he said.
