The Hernandez family plans to donate the brain to Boston University to undergo testing as part of the university's concussion research but lawyer Jose Baez said the medical examiner is "illegally" holding the brain.
The medical examiner released Hernandez's body to a funeral home on Thursday but didn't include the brain.
"It is our position that they are holding Aaron Hernandez's brain illegally," Baez told reporters. "There is a fixing procedure to prepare these specimens. It is their position that they are going to be the ones to do the fixing procedure. The family does not have confidence in the medical examiner's office."
The medical examiner's office declined comment.
Baez said the family decided on giving the brain to Boston University to see if there are signs of chronic traumatic encephalopathy (CTE) in Hernandez's brain. CTE is the debilitating brain disease that researchers say is caused in part by concussions while playing football and other head trauma.
"The family of Aaron Hernandez has decided to donate Aaron's brain to the study so we can possibly help other young men who play football ... further the cause, and possibly shed light and provide more evidence on this case," Baez said.
Hernandez's apparent suicide occurred just five days after he was acquitted on double-murder charges. The timing of his death -- prison officials say he hung himself -- has perplexed people and Hernandez didn't leave a suicide note.
"There were no conversations or correspondence from Aaron to his family or legal team that would have indicated anything like this was possible," Baez said. "Aaron was looking forward to an opportunity for a second chance to prove his innocence. Those who love and care about him are heartbroken and determined to find the truth surrounding his untimely death."
Hernandez was serving a life sentence for the murder of Odin Lloyd, a sentence delivered in April 2015.
Guards discovered the 27-year-old Hernandez in his single cell at the Souza-Baranowski Correctional Center in Shirley just after 3 a.m., the Massachusetts Department of Corrections said.
The former University of Florida and NFL star was pronounced dead at UMass Memorial-HealthAlliance Hospital in Leominster.
Hernandez was in a maximum security state prison not far from the Patriots' home, which is in Foxborough, Mass.
Corrections officers said Hernandez hung himself using a bed sheet that he attached to a cell window.
Hernandez was emotional Friday as the jury read a not guilty verdict acquitting Hernandez of the 2012 fatal shootings of Daniel de Abreu and Safiro Furtado in Boston.
A fourth-round draft pick in 2010, Hernandez signed a seven-year, $40 million contract with the Patriots prior to the 2012 season. That deal included a $12.5 million signing bonus and $15.9 million guaranteed.
Hernandez's death occurred on the same day the Patriots visited the White House to mark their Super Bowl LI comeback win over the Atlanta Falcons.