In addition to Lee, the police arrested a friend of Phagan's for the crime. Gradually, the police became convinced that these were not the culprits. By Monday, the police had theorized that the murder occurred on the second floor (the same as Frank's office) based on hair found on a lathe and what appeared to be blood on the ground of the second floor.
Both Newt Lee, after the discovery of Phagan's body, and the police, just after 4 a.m., had unsuccessfully tried to telephone Frank early on Sunday, April 27. The police contacted him later that morning and he agreed to accompany them to the factory. When the police arrived after 7 a.m. without telling the specifics of what happened at the factory, Frank seemed extremely nervous, trembling, and pale; his voice was hoarse, and he was rubbing his hands and asking questions before the police could answer. Frank said he was not familiar with the name Mary Phagan and would need to check his payroll book. The detectives took Frank to the morgue to see Phagan's body and then to the factory, where Frank viewed the crime scene and walked the police through the entire building. Frank returned home about 10:45 a.m. At this point, Frank was not considered a suspect.
On Monday, April 28, Frank, accompanied by his attorney, Luther Rosser, gave a written deposition to the police that provided a brief timeline of his activities on Saturday. He said Phagan was in his office between 12:05 and 12:10 p.m., that Lee had arrived at 4 p.m. but was asked to return later, and that Frank had a confrontation with ex-employee James Gantt at 6 p.m. as Frank was leaving and Lee arriving. Frank explained that Lee's time card for Sunday morning had several gaps (Lee was supposed to punch in every half-hour) that Frank had missed when he discussed the time card with police on Sunday. At Rosser's insistence, Frank exposed his body to demonstrate that he had no cuts or injuries and the police found no blood on the suit that Frank said he had worn on Saturday. The police found no blood stains on the laundry at Frank's house.