The source gave no indication whether there was any connection between that investigation and Hernandez's current murder charge.
What is known is that the Boston Police Department has located and impounded a silver SUV with Rhode Island registration that police have been trying to find for almost a year, that's linked to the scene of a double homicide in 2012, the source said.
Investigators believe that Hernandez was renting the SUV at the time of those killings, the source said.
Hernandez, who was released by the New England Patriots on Wednesday after his arrest, will be back in a courtroom Thursday for a bail hearing.
Hernandez is scheduled to appear at Fall River, Massachusetts, Superior Court at 2 p.m. to appeal a judge's decision to hold him without bail, the court magistrate said.
A second man arrested in connection with the killing of Odin Lloyd is also expected to appear before a judge.
Carlos Ortiz was arrested in Bristol, Connecticut, on Wednesday and will have an initial hearing in Attleboro, Massachusetts, District Court as early as Thursday, a source with knowledge of the investigation told CNN.
Hernandez is accused in last week's shooting death of Lloyd, whose body was found in an industrial park area less than a mile from Hernandez's home.
He has pleaded not guilty.
Accusation of orchestrating murder
Hernandez "drove the victim to the remote spot, and then he orchestrated his execution," First Assistant District Attorney Bill McCauley said in court Wednesday.
"He orchestrated the crime from the beginning, he took steps to conceal and destroy evidence, and he took steps to prevent the police from speaking to ... an important witness," the prosecutor said.
Defense attorney Michael Fee has said that the evidence is circumstantial and that bail should be granted so that Hernandez can return home to spend time with his fiancee and 8-month-old child.
"It is a circumstantial case. It is not a strong case," Fee said, arguing that Hernandez was not a flight risk and had cooperated with authorities.
Lloyd, 27, was a semipro football player who worked for a landscape company. His sister, Olivia Thibou, told CNN last week that her brother was dating the sister of Hernandez's fiancee. Lloyd and Hernandez were at a Boston nightclub together the night of June 14, she said.
A 'model inmate'
During his first 24 hours in jail, Hernandez has been "polite and cooperative" and a "model inmate," Bristol County Sheriff Tom Hodgson said.
Hernandez was being held in the jail's medical unit, which is standard for someone who hasn't been incarcerated before, Hodgson said.
The former pro athlete showed "no apparent nervousness" in jail, Hodgson said, but he noted the difficulty of going from having thousands of people cheering for him to being "just a number."
While in the medical unit, Hernandez will be locked up for 23 hours a day, with a break for a shower and phone calls, the sheriff said.