The FBI and Shakopee police are jointly investigating former Shakopee schools superintendent Rod Thompson, who allegedly admitted to accepting perks from companies working with the School District, according to a search warrant affidavit filed this week.

The south metro district’s school board accepted Thompson’s resignation in June after police began investigating personal purchases he allegedly made using a district credit card.

Authorities are now investigating allegations that Thompson received kickbacks, including vacations and loans, from at least three companies that were awarded contracts with the district, according to the affidavit for the search carried out Wednesday.

Shakopee police Sgt. Fred Radde said Thursday that the department cannot comment on the nature of its collaboration with the FBI.

Detective Jim Blatzheim filed this week’s affidavit — the second in the case — seeking to search the district office for information on Thompson’s e-mail account after citing repeated verbal requests to the district that he said were rebuffed. Blatzheim wrote that on Wednesday, he downloaded Thompson’s e-mail account from a computer in the district office to an external hard drive to be examined by investigators.

The first search warrant affidavit in the case went to district attorney Peter Martin on June 13. Martin did not provide all of the e-mails sought, providing only received or inbox e-mails, according to the affidavit filed this week.

Martin told investigators that Thompson received “200 e-mails every day” and asked them for the second search warrant, citing the Family Educational Rights and Privacy Act, which protects the privacy of student records.

Shakopee police began looking into Thompson’s spending history in May upon receiving a citizen’s complaint and learning about an investigation into Thompson by the Shakopee Valley News. Detectives then obtained documents from as far back as February 2012 from the district’s bank, the Bank of Montreal, which showed multiple personal purchases made by Thompson, according to the affidavit.

Thompson told investigators about his personal purchases and a September 2016 trip to Nashville with his wife. He had allegedly made purchases totaling more than $3,500 during his time as superintendent.

Police searched Thompson’s residence in June and left with a TV, a laptop and a Kindle. The June search warrant affidavit listed multiple district employees who had told investigators that Thompson did not respond to requests for receipts of his purchases.

Thompson’s resignation was effective June 30. The school board approved his separation agreement for $50,000 on June 19. The board is now narrowing its list of finalists for an interim superintendent.

Community residents launched their own investigation into Thompson in March when the then-superintendent sent an e-mail to staff members notifying them of a $4.5 million budget error he described as “human error.”

School board Chairman Scott Swanson declined to comment Thursday on the current investigation.