Judge Marsha Revel, who sentenced the actress to 90 days in jail and three months in rehab, voluntarily removed herself from the case last Friday.
"The prosecutor raised objections about the judge having hearings and conference calls without having the DAs present or being notified," Los Angeles District Attorney spokeswoman Jane Robison told PEOPLE. "It happened several times."
In one particular instance, Judge Revel made a last-minute change regarding the rehab facility where Lohan should receive treatment, and didn't notify the prosecutor.
Revel has been replaced by Judge Elden Fox, who is no stranger to celebrity cases, having overseen Winona Ryder's shoplifting trial, a drug possession case of Courtney Love's and Lane Garrison's vehicular manslaughter case.
Lohan, 24, remains in treatment at UCLA Medical Center and is not expected to be released until early November.
The actress's attorney, Shawn Chapman Holley, had no comment.