The father called the West Hollywood sheriff's station about 11:30 a.m., saying he was concerned about his 16-year-old daughter, according to a statement from the Los Angeles County Sheriff's Department.
Although it's unclear whether Ali lives with Lindsay, Ali was with her sister at the time of the call, which led deputies to go to the 23-year-old actress' apartment. Lindsay was "very cooperative" and allowed officers in, said Nicole Nishida, a spokeswoman for the sheriff's department.
Both Lindsay and Ali spoke with the officers, who determined Ali was not in danger, Nishida said.
The sheriff's department would not comment on whether the 49-year-old father — who went to the house with the deputies, according to TMZ — was allowed into the apartment as well, or if he had any interaction with either of his two daughters.
Lindsay tweeted her frustration during the incident, writing: "I have no choice but to make this public, due to my sister's safety, as well as my own, 'my ex-dad' just WALKED INTO MY APT like the devil's ... advocate with officers."
Lohan also called her father "crazy" and accused him of past drug use. "When will it ever end?" she wrote. "It's been going on my whole life with him — hasn't he caused enough pain?"
Michael Lohan said his main concern was Lindsay and he began to fear for Ali's well-being after learning she was under her sister's care.
"I've been on a mission to get Lindsay to get help. Then I found out Ali was here and that they drove back from Coachella this weekend going over 100 mph," Lohan told TVGuide.com. "One of Lindsay's friends [was driving]. But that's ridiculous! Ali is 16 years old. She is still a minor.
Lohan said he had planned to try to reach out to his daughters on Wednesday, and flew to Los Angeles specifically to speak with them.
"I went to the sheriff's office at 8:30 this morning," he said Thursday. "He said, 'Well, if you want to go and check on your daughter's welfare, you have a right to do that within the law and we will go with you. We can't gain entry on the place, but we can ask.' The manager freely gave us the key to the place. We went up there, knocked on the door, said we were with the sheriff and want to make sure Ali's OK."
(Additional reporting by Joyce Eng)