Superintendent Jimmy Weeks confirmed Tuesday that he'd suspended Capps with pay last week.
"I put him on administrative leave," Weeks said, when asked about Capps' status.
Later in the afternoon, the district's school board voted to put Capps on unpaid leave.
Messages left with Capps on Tuesday were not immediately returned.
Weeks said his decision was directly related to the ongoing investigation, which brought the arrest April 17 of longtime business manager, Randy Thweatt.
Auditor Stacey Pickering accused Thweatt of embezzlement involving the alleged installation of a school district air-conditioning unit at a mobile home Thweatt owns in Starkville and with a pickup truck's title change from the school district to Thweatt earlier this year.
Neither the District Attorney's Office nor the auditor's office would say anything about the investigation, or provide any insight into Capps' status.
Assistant District Attorney Paul Howell said late Tuesday that while the investigation continues, no arrests or other charges have come forward yet.
After Thweatt's arrest, Pickering's office said its investigators have four "targets" under scrutiny for alleged wrongdoing involving the school district.
Weeks said he suspended Capps "after I talked with the investigators," who indicated the district's transportation department was part of their focus.
"I felt like it was the best thing for the district and for Mr. Capps to be on leave," said Weeks, whose term as the district's elected head began in January. "We've done what we can do."
patsy.brumfield at journalinc.com
Business manager's indictment made public
TUPELO – Randy Thweatt, longtime business manager for the Lee County School District, has been formally indicted on embezzlement charges.
Paul Howell with the District Attorney’s Office in Tupelo said Thweatt was indicted by a March grand jury on two counts alleged in his April 17 arrest by the auditor’s office. The indictment was made public Tuesday.
He had been placed on paid leave from the school district last week and remains free on bond, but with the indictment Tuesday the school board changed his leave status to unpaid.