Sherin Mathews, who has developmental issues and limited verbal communication skills, was last seen outside her family's backyard in Richardson, Dallas.
Richardson police along with an FBI evidence recovery team entered the house of Wesley Mathews last night to execute a search warrant, police Sergeant Kevin Perlich said.
The search was part of the "natural progression" of the investigation, he was quoted as saying by the Dallas Morning News.
Investigators will process what they have collected, including security footage, electronics and items in the family's three vehicles that were towed from the home, Perlich said.
Sherin's father, Mathews, 37, was arrested on Saturday on a charge of abandoning or endangering a child. He was released from custody on Sunday after posting USD 250,000 bond.
He is required to wear an electronic monitoring device and surrender his passport as part of the conditions of his bond, the paper said.
Meanwhile, officials with Texas Child Protective Services removed the toddler's 4-year-old sister from the family on Monday and placed her in protective custody as police continue to search for the missing child.
Mathews, said to be from Kerala, told police that he put Sherin outside and told her to stand next to a large tree about 3 am on Saturday, an arrest-warrant affidavit said.
The tree was behind a fence, about 100 feet south of the family's home and across an alley.
Mathews admitted to police that he knew coyotes had been seen in the alley, the affidavit said.
Mathews told the police that he checked on Sherin about 3:15 am and she was gone, the affidavit said.
Police were not alerted to her disappearance until about five hours later.
"Why was the last sighting at 3 o'clock and the parents not call us until after 8 am, that's the question we want answered as well," Perlich told KXAS-TV NBC5.
"As far as why she was out there, how long she was out there, that's the questions we have for the parents."
The girl's mother does not face any charges. She was in the house at the time, but was reportedly asleep and unaware of what Wesley Mathews was doing, Perlich said.
"I don't know what happened," said Philip Mathew, Sherin Mathews's great-uncle.
The Mathewses reportedly adopted the girl two years ago from an Indian orphanage. She was malnourished and physically underdeveloped and does not have the same language skills a typical 3-year-old would in the US, Perlich said.
He told NBC5 it was not unusual for her to be awake late at night to eat to increase her weight.
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