Assistant Rexburg Police Chief Gary Hagen told reporters that Daybell was being questioned after a search warrant was served on his home. He said that detectives had recovered unidentified human remains in their investigation of the missing children.
Hagen did not provide additional details about the warrant, which was sealed. Media was not allowed near the home during the search.
Police confirmed to KTVB that the search warrant is related to the disappearance of JJ Vallow and Tylee Ryan, who were 7 and 17 years old respectively when they went missing in September.
In a December statement, police said Vallow and Daybell were refusing to cooperate with the investigation into the missing children that began in November, and that they had left the state.
Police have said Vallow either knows the location of her children or knows what happened to them.
After Vallow and her husband were found in Hawaii, she was arrested in February and extradited to Idaho on charges of desertion and nonsupport of dependent children. She is being held on a $1 million bond.
Vallow has pleaded not guilty to the charges, according to The Associated Press.
Vallow is also being investigated for murder, attempted murder and conspiracy in the death of her husband's former wife.
Tammy Daybell's body was found in her home in October, a death initially ruled as natural but since classified as suspicious.
In December, the 49-year-old's remains were exhumed so an autopsy could be conducted, the results of which are still pending, according to KTVB.
Chad Daybell, a self-published author who has written more than two dozen books about near-death and doomsday events, and Vallow married weeks after Tammy Daybell's death. They have not been charged in that case.
Vallow's fourth husband, Charles Vallow, also died last year. He was shot to death in July by Vallow's brother, Alex Cox, during a confrontation.
Vallow and Cox were questioned by police but not charged. Cox then died in December.