The Department of Children and Family Services said it was investigating whether there were “shortcomings” in the agency’s oversight of a 5-year-old boy whose body was found Wednesday a few miles from his home in Crystal Lake.

Andrew “AJ” Freund’s body was discovered Wednesday in a shallow grave in northwest suburban Woodstock and authorities have charged his parents, JoAnn Cunningham and Andrew Freund Sr., with multiple counts of murder in their son’s death.

Officials have not released a cause of death for Andrew pending an autopsy that was expected to take place this week, but both parents have additionally been charged with aggravated battery and aggravated domestic battery, according to Crystal Lake police.

In a statement Wednesday afternoon, Acting DCFS Director Marc Smith said the agency was “committed to conducting a comprehensive review of the entirety of our work with Andrew’s family to understand our shortcomings and to be fully transparent with the public on any steps we are taking to address the issues.”

THE FREUND INVESTIGATION:

• Parents charged with murder after Andrew ‘AJ’ Freund found dead

• Missing boy, 5, lived in Crystal Lake home full of dog feces, records show

• Family of missing Crystal Lake boy has lengthy history with DCFS: officials

• FBI searching for missing 5-year-old from Crystal Lake

A spokeswoman from the DCFS did not immediately respond to messages left after the statement was delivered.

DCFS first became involved with the Freund family when Andrew was found to have opiates in his system after his birth in 2013 and was put into foster care, agency officials said after the boy was reported missing by his parents on April 18.

At the time, Cunningham was involved in a legal dispute with her mother for custody of the boy, the Northwest Herald reported. The boy’s grandmother filed a petition for an order of protection, the paper said, accusing the boys’ parents of denying him medical care, food, clean clothing and a healthy living environment. He lives in “constant fear, hunger and filth,” the petition claimed.

DCFS, though, returned the boy to his parents in June 2015, officials said. Twice last year, DCFS caseworkers returned to Andrew’s home to investigate separate allegations of neglect, though both were determined to be unfounded.

Last Thursday while still searching for Andrew, authorities took custody of his younger brother, who was placed in another home under a DCFS safety plan, the agency said.

The most recent investigation by caseworkers appears to have been in December when police officers responding to a reported theft at the house found the home “cluttered, dirty and in disrepair,” according to five years of Crystal Lake Police Department records.

The reports show officers found the home to be scattered with dog feces and urine, with broken windows, jagged holes in the kitchen to the sub-floor and a leaking pipe in the kitchen ceiling, as well as a unknown brown substance covering a rear door.

When one officer noticed a bruise on one of the boys legs, they placed Cunningham under arrest for driving with a suspended license and took her and her sons to the police station. According to the report, a DCFS caseworker was unable to determine what caused the bruise, which the boy and his mother both said could have been caused by the family’s pet dog, Lucy.

A follow-up examination by medical personnel was also inconclusive, the report said.

Officers had been to the home just months earlier in September after a concerned citizen reported the family had been living without power for weeks.

Cunningham admitted to the officers that the home was without power, but said she did not know how long it had been out and told them she was often staying elsewhere, including an area motel. She did not allow the officers inside, according to the police report, but an officer reportedly saw both children and believed they appeared to be healthy and happy.

In the police report for that incident, an officer wrote that DCFS told the department that they would not come out for a wellbeing check for a utility issue alone. Police were awaiting clarification from DCFS but said that no one from the agency had called the department back by the time the report was finalized.

Cook County’s Public Guardian accused the child protection agency in March of “major failures” after 2-year-old Ja’hir Gibbons was beaten to death at his Chicago home while his family was under DCFS oversight. The criticism came a day after the agency announced it was investigating allegations that a contracted caseworker with Buffalo Grove-based Omni Youth Services had falsified records related to Ja’hir after his death.

Gov. J.B. Pritzker at the time called the boy’s death a tragedy and said that it could have been prevented by reducing the caseloads of DCFS workers.

“The additional issue here is that there’s an individual and an agency that have made gross mistakes,” Pritzker said. “The investigation that’s ongoing now is intended to make transparent what those challenges were and how we should address them.”

A week later, Pritzker announced he was appointing Smith, the former executive vice president of foster care and intact services at Aunt Martha’s Health & Wellness, to lead the agency.

“This news is heartbreaking,” Smith said of the Freund case in the statement provided Wednesday. “Protecting vulnerable children who come to our attention is at the core of our mission at DCFS. All of us feel this loss. Our priority is the care and safety of Andrew’s younger sibling.”

Chapin Hall, a policy research institute at the University of Chicago, has also been asked by the governor to conduct a review of the agency’s Intact Family Services Unit.

On Wednesday, a spokeswoman for Chapin Hall said she could not comment on Andrew’s case due to their ongoing inquiry into DCFS but said she expected their report to be released next month.