Philip Haney, who spoke out against his own agency during the Obama administration, was found in a park and ride area near Plymouth, California, with what the Amador County Sheriff's Office initially said appeared to be a self-inflicted gunshot wound.
However, those initial reports have been described as “misinformation” and have been walked back in a statement from the sheriff's office, which also confirmed the FBI will be assisting the investigation.
A forensic autopsy is scheduled to be performed by the Sacramento County Coroner’s Office.
The FBI will assist in examining documents and a laptop found at the scene, as well as phone records. The agency will also help with evidence processing on Mr Haney’s motorhome and the firearm.
The location is just three miles from where Mr Haney was living in a motorhome park and his neighbours have been canvassed and video surveillance collected.
Mr Haney gained national attention in 2016 when he criticised the DHS for its handling of radical jihadists and Islamist extremists.
In testimony before the Senate Judiciary Committee, he alleged that the Obama-era DHS had ordered him to delete hundreds of files about reputed associates of Islamist terrorist groups.
He claimed that several attacks in the US could have been prevented if some of the files had not been deleted. He retired in 2015.
The Washington Examiner reports that he planned a sequel to his memoir of his time at DHS, See Something, Say Nothing: A Homeland Security Officer Exposes the Government's Submission to Jihad.