The anonymous writer claimed to be a student at a district high school who had been bullied. New York City officials concluded the threat was a hoax and declined to close schools.
New York police commissioner and former LAPD chief William Bratton said he thought Los Angeles officials overreacted.
Update, 10:45 a.m.:
The White House says the different reactions taken by the nation's two largest public school systems after receiving threats show that local first responders are responsible for protecting their communities.
Spokesman Josh Earnest says he won't "second-guess" the decisions by Los Angeles officials to close their schools and New York City officials to keep their students in class.
Earnest says local authorities make decisions based on information they receive and what they believe is in the best interests of their communities.
Los Angeles law enforcement and city leaders defended the decision to shut down the city's school system due to an emailed threat.
Police Chief Charlie Beck and Mayor Eric Garcetti told reporters that they stand behind the superintendent's order to close the Los Angeles Unified School District's more than 900 schools and 187 public charter schools as a precaution.
The nation's second-largest school district shut down all of its campuses Tuesday after an emailed threat targeted students at many Los Angeles-area schools.
The shooting in nearby San Bernardino that left 14 people dead this month influenced the decision to close all the schools in the Los Angeles Unified School District, which 640,000 students attend, Superintendent Ramon Cortines said.
New York City officials say they received the same threat, but quickly concluded that it was a hoax. New York Police Commissioner William Bratton said he thought Los Angeles officials overreacted.
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.
A law enforcement official says the threat was emailed to a school board member late Monday and appeared to come from overseas. The official spoke on condition of anonymity because he was not authorized to speak publicly about the investigation.
Officials in Los Angeles would not elaborate on the threat, saying it was still being evaluated, but said the shutdown came as a precaution. Schools would remain closed until the threat was cleared, which could happen by the end of the day, officials said.
Los Angeles schools commonly get threats, but Cortines called this one rare.
"It was not to one school, two schools or three schools," he said at a news conference. "It was many schools, not specifically identified. But there were many schools. That's the reason I took the action that I did. ... It was to students at schools."
Cortines said he wants every campus to be searched and a report given to him and the school board that they are safe. The district has more than 900 schools and 187 public charter schools.
The superintendent said the district police chief informed him about the threat shortly after 5 a.m.
"He shared with me that some of the details talked about backpacks, talked about other packages," Cortines said.
No students would be released on their own, and school leaders would wait with children whose parents had not yet arrived to pick them up, he said.