The Education Funding Agency finalised an investigation into the financial management of the Priory Federation of Academies, formed out of four county academies.
The Department of Education said that as a result, Richard Gilliland, chief executive at the federation, resigned on March 30.
The findings of the investigation have not been made public.
The federation was formed in 2008, made up of four schools: Priory Academy LSST, Priory Witham Academy, Priory City of Lincoln Academy and Priory Ruskin Academy.
As Priory Federation of Academies chief executive, Richard Gilliland was reportedly earning more than £200,000 per year, one of the county’s highest paid public servants.
He cited personal reasons for his resignation, just before schools broke up for Easter.
Deputy chief executive Ian Jones has taken on the role of CEO on an interim basis, alongside his post as headteacher of The Priory Academy LSST.
The Priory said day-to-day running of the schools remains unchanged.