Trista Reynolds told ABC's "Good Morning America" that she and Ayla Reynold's father have been unable to get along in the last few weeks. She said she didn't tell the father, Justin DiPietro, that she'd filed the court paperwork Thursday.
"I've had no contact with him; he's had no contact with me. All I know is he's the last man to see my daughter, and all I want to know where she is," she said Monday.
A phone number for Justin DiPietro couldn't immediately be located. Police were posted outside his house on Monday and said DiPietro was not home.
Over the weekend, police appealed for the public's help in finding the youngster after the father called police Saturday morning to report that his daughter was not in her bed and couldn't be found. Ayla was last seen Friday night.
On Monday, the Maine Warden Service was focusing its search efforts on Messalonskee Stream, which passes a few blocks from the father's home. The FBI and Maine State Police were also assisting Waterville police, said Steve McCausland, spokesman for the Maine Department of Public Safety.
Ayla, who's blond and 2 feet 9, was last seen wearing green one-piece pajamas with polka dots and the words "Daddy's Princess" on them. She had a soft cast on her left arm; Waterville Police Chief Joseph Massey said Ayla broke her arm in a fall three weeks ago.
Massey said investigators interviewed the father, who lives in Waterville, and the mother, who lives in Portland, as well as other family members. He said they all were cooperative.
Authorities interviewed neighbors and searched the area Saturday and Sunday. They also used a search dog at the girl's house to make sure she was not hidden in a closet or some other small space, Massey said.
The police chief said all possibilities were being investigated, including abduction.
"Everything is open. Everything is on the table," he said. "We have not uncovered any information that has sent us in any direction."
Waterville is about 20 miles north of Augusta.