(CNN) -- Police believe they found the skeletal remains of a 3-year-old Alabama boy and were charging his father with two counts of murder as they prepared to search for the man's missing young daughter, also believed dead, authorities said Wednesday.
Authorities are working to verify the remains found Wednesday near Vancleave, Mississippi, belong to Jonathan Chase DeBlase. Police believe he was killed by his father, John Joseph DeBlase, 27, and the father's girlfriend.
Jonathan had not been seen since June, police in Mobile, Alabama, said. Investigators believe he was slain around that time. His sister, 4-year-old Natalie, was last seen in March, when authorities believe she was killed. Earlier, police had reversed the order of the last sightings of the children, but they clarified that timeline Wednesday.
Police, who did not know the children were missing until November 19, contend that the elder DeBlase allowed the girlfriend, Heather Keaton, to abuse the children by restraining them with tape, putting socks in their mouths and confining them.
The boy's skeletal remains were found about 12 miles north of Vancleave, after the boy's father -- who is in police custody in Alabama -- gave authorities information on where the body might be buried, said Jackson County, Mississippi, Sheriff Mike Byrd.
"It was the father who gave us the general area," Byrd told HLN. "He wasn't real sure exactly where he was. ... He claimed he had taken a lot of sleeping pills and didn't quite remember exactly where he was."
Based on that information, the sheriff's office cordoned off a five-mile stretch along a highway and dispatched eight 10-man teams to locate the remains. The body was found about 10:30 a.m., Byrd said.
"We're very certain" the remains are that of the missing boy, Byrd said. "We're just thankful that we found this little boy. Nothing's left but just the skeletal remains."
The body of Natalie DeBlase has not been found, Byrd said, but he indicated authorities believe it near Citronelle, Alabama, about 50 miles north of Mobile.
A spokesman for Mobile Police told HLN that prosecutors are signing two murder warrants against John DeBlase.
Authorities will decide in the next few days whether to charge Keaton in the deaths, Officer Christopher Levy said.
Police believe both children died in Mobile, Levy said.
Levy was not sure when the search for Natalie near Citronelle will begin in earnest.
"This is a one-step-at-a-time, one-day-at-a-time operation," Levy said. "We've had some success with it today. We're going to evaluate our results, then begin the next step."
Levy said he was relieved at the new findings, but said the investigation had taken a toll.
"I have kids that are of similar age and it makes me think about them while I'm out here," Levy told HLN.
Investigators believe that after Jonathan's death, John DeBlase, Keaton and Natalie continued to live in the Peach Place Apartments in Mobile for months, Levy said Monday. They didn't leave until the summer, after Natalie was last seen in June.
"It's really terrible, as if nobody really cared," Levy said of the time that transpired between the sightings and launch of the search. "That's what we can't seem to understand at this point."
Both DeBlase and Keaton are now in custody, and blaming each other for the siblings' deaths.
The investigation kicked off November 18, when Keaton told Louisville, Kentucky, police that she needed protection from DeBlase, who she claimed was holding her against her will.
According to the domestic violence petition, signed "Heather L. Leavell-Keaton," she said, "I feel he may have murdered his children, because he said they were non-responsive. He would not let me check on them." She said DeBlase had told her "choices were made ... and he had to do what he had to do."
Keaton was arrested last week, charged with two counts of willful abuse and neglect of a child.
Three days later, Randall Melville -- who for two days had been hosting DeBlase, his longtime friend -- called Santa Rosa County, Florida, police after hearing news reports about the children's disappearance, according to a report from the county sheriff's department.
When Melville asked DeBlase about it, the children's father yelled, "I didn't do it" and left the home, the report said. Police eventually tracked down DeBlase, who again asserted his innocence before his arrest Friday.
He had been charged with two counts of aggravated child abuse and two counts of abuse of a corpse -- the latter because, Levy said, of his "disposing of the bodies in the woods."
DeBlase had a first appearance on the abuse charges Wednesday and a judge entered a not guilty plea, said Jim Sears, who was assigned to represent the father at the Mobile proceedings.
Sears described his client as being very upset about developments. A preliminary hearing is scheduled for January 4.
On Monday, Mobile County District Judge Charles McKnight set bail for DeBlase at $206,000 -- $100,000 each for the child abuse charges and $3,000 for each count of corpse abuse, according to CNN affiliate WALA.
According to a police complaint, DeBlase between March 1 and November 19 allowed Keaton to tape Natalie's hands and feet, put a sock in her mouth and place her in a suitcase that was put in a closet for 14 hours. He also allowed Keaton to tape Jonathan's hands to the side of his legs, tape a broom handle to his back, place a sock in his mouth and then make the child stand in a corner all night when the couple went to bed.
DeBlase and Keaton had one infant daughter together, according to Keaton's account in the Kentucky police report. Police said one reason Keaton claimed she needed protection from DeBlase was that she feared for the safety of the infant, who was with her in Kentucky.
Levy said the two slain children's biological mother lives in Mobile, but she did not have custody "because, at the time, she didn't have a place to live."
CNN's Natisha Lance, Vivian Kuo, Beth Carey and Andy Rose contributed to this report.