Los Angeles County Sheriff's Department spokesman Steve Whitmore confirmed the second arrest but would not immediately release any information on the reason.
The second teacher was removed after someone made accusations against him, Los Angeles Unified School District Superintendent John Deasy said in a statement.
He declined to provide details on the second educator.
Child-abuse investigators were informed by the district late Thursday night, sheriff's Lt. Carlos Marquez said, declining to provide details.
Earlier this week, third-grade teacher Mark Berndt, who worked at the school for 30 years, was charged with committing lewd acts on 23 children, ages 6 to 10, between 2005 and 2010. He remains jailed on $23 million bail and could face life in prison if convicted.
Deasy wouldn't discuss the allegations against the second teacher or whether it was sexual.
"This just came to our attention yesterday," Deasy said Friday. "The information was new. It's not, like, something we dug up."
He also said that the teacher was removed from class "out of an abundance of caution" rather than because of any physical evidence.
"This would be what I would call a normal course of action."
"In the Berndt case, allegations came forward with photographs and evidence, so to speak. That is not the case."
Deasy said the district has seen an increase in the number of complaints of teacher molestation since news of Berndt's arrest broke, but he provided no figures.
School was in session Friday at Miramonte. After news broke about the second teacher, several parents took their children out of school.
Ida Santana said her sister called her and told her to pick up her nephew.
"It's hard to leave our kids here," Santana said. "We can't trust the teachers no more. Now there's another teacher."
Several other parents could be seen walking youngsters away from the school.
Santana said the family is unsure where the boy will be going to school from now on.
The development involving the second teacher was made public a day after authorities acknowledged that 18 years ago a 10-year-old girl claimed Berndt tried to fondle her.
Prosecutors declined to file to charges against Berndt in the 1993 report, saying they didn't have enough evidence.
The details of that case and other claims by two former students about strange behavior by Berndt surfaced just three days after his arrest.
The allegations also raised further questions about why he wasn't disciplined by school officials, who have been lambasted by some parents for waiting a year to reveal Berndt was suspected of taking bondage-style photographs of children in his class.
Only parents of children identified as victims were told by authorities about the most recent investigation.
School officials and investigators said proper procedures were followed to investigate and build a case against the teacher.
The incident involving the 10-year-old girl occurred in September 1993 but wasn't reported by her mother to officials at Miramonte until the following January, after her daughter had seen an "Oprah" show about inappropriate touching, Los Angeles County sheriff's Sgt. Dan Scott said Thursday.
The girl claimed Berndt reached toward her genitals during class and she pushed his hand away, Scott said.
School officials notified the Sheriff's Department, which submitted evidence to prosecutors. They opted not to file a charge of committing a lewd act on a minor under the age of 14. Berndt was never arrested.
"Based on what I read, it was a thorough and complete investigation," said Scott, who noted the investigator who handled the case has retired.
Sandi Gibbons, a district attorney spokeswoman, said in a statement the case was rejected because there was insufficient evidence to prove a crime had occurred. The statement did not elaborate.
Berndt denied the allegation at the time.
Earlier, two women who said they were former students of Berndt told the Los Angeles Times that complaints were made about his odd behavior as far back as 1990.
Using a cheap camera, Berndt is suspected of snapping nearly 400 photographs of Miramonte students, some with a giant Madagascar cockroach from a classroom terrarium on their faces.
Others were blindfolded or had clear tape over their mouths, and some were given sperm-laced cookies to eat as treats in the photo sessions that were treated like games, Scott said.
Some of Berndt's students defended him, saying he was a kind and generous teacher.
Angelica Zuniga, a 16-year-old high school junior, was in third grade in 2003 when she had Berndt as a teacher. She said he never asked her or others to do anything strange or to play any inappropriate games.
"They're calling him 'monster.' He's just not that kind of person," Angelica said. "He was one of the most amazing teachers out there. He's dedicated his life to us, and I want to stick up for him."
The latest investigation of Berndt began last fall when a film processor became suspicious about the photographs and turned them over to Redondo Beach police, who on Dec. 2 handed them over to the sheriff's department, Scott said.
Berndt, who taught at Miramonte for more than 30 years ago, was removed from classwork in January and fired within the month.
The case also prompted Deasy to fire a high school teacher who is being sued over allegations he had sex with students. The Los Angeles Times reported Friday that Vance Miller, 59, was pulled from his Hamilton High School classroom in 2010, before Deasy became superintendent.
A police investigation didn't result in criminal charges. But two former students, now adults, said the music teacher had sex with them while they were students at Hamilton. Deasy reviewed the case this week and decided there was enough information to fire Miller, who has been paid since his removal.
Associated Press writers Christina Hoag, Robert Jablon and Raquel Maria Dillon contributed to this report.