Phillips said Wednesday in a statement released by ESPN that he requested the leave "to address this with my family and to avoid any unnecessary distractions through the balance of the baseball playoffs."
ESPN said it took "appropriate disciplinary action" when this happened in August, but would not comment further.
Police say 22-year-old ESPN production assistant Brooke Hundley began calling Phillips' wife, Marni, on Aug. 5 after he broke off the affair and sent her a letter graphically describing their relationship and Phillips' birthmarks. She allegedly told Phillips' wife that "we both can't have him," according to a Wilton, Conn., police report.
"I'm a real person in his life and I care deeply about his happiness," reads the letter police said is from Hundley. "I'm coming out now because I'm sick of hiding and sneaking around behind your back."
The police report was first reported Wednesday by the New York Post.
The 46-year-old Phillips is a former general manager of the New York Mets. In 1998, Phillips admitted having sex with a team employee, who sued for sexual harassment. That case was settled out of court.
Marni Phillips called police Aug. 19 when she came home to find Hundley in her driveway. "I knew instinctively that this was the woman Steve was involved with and I was terrified," she wrote in a statement to police.
Hundley's car smashed into a stone column as she backed out of the driveway and she escaped by driving across the lawn. Marni Phillips said she discovered a note describing her husband's relationship with Hundley attached to her front door.
Later that evening, the Phillips' 16-year-old son told his parents that Hundley had posed as a high school classmate and sent repeated instant messages asking personal questions about his family and his parents' marriage, according to the police report. She also posed as a second friend, contacting him through the son's Facebook account, the report said.
"This woman has clearly displayed erratic behavior and delusional tendencies," Phillips said in a statement to police. " She has shown up at our house. She has taken on the identity of at least two people (minors) to violate our son (a minor). I have extreme concerns about the health and safety of my kids and myself."
Phillips also signed a statement to police that he would not press charges. The status of the police investigation was unclear Wednesday. The report indicated a detective planned to interview Hundley next week when she returned from vacation.
Neither Phillips, Hundley nor Wilton police immediately returned calls Wednedsay from the AP. ESPN said Hundley is still employed at the network.
According to the Wilton police report, Phillips told police and his wife about the affair after being pressed to do so by Hundley. He said the affair was three meetings that all took place in July. Marni Phillips told police she had received "harassing phone calls and text messages" from a woman who claimed to have information about her husband.
Marni Phillips filed for divorce Sept. 14, according to court records.
Phillips is the latest ESPN personality entangled in workplace issues involving alleged misconduct. In 2006, baseball analyst Harold Reynolds was fired after a female intern complained about what he called a "brief and innocuous hug." Reynolds sued and settled with the network last year.
Last year, a judge dismissed a lawsuit filed by a makeup artist who accused hosts Jay Crawford and sports writer Woody Paige of groping and propositioning her on the set of the now-defunct show "Cold Pizza."