FIFA announced that it dismissed its deputy secretary-general, Markus Kattner, on Monday evening.
The world footballing body said its firing of the 45-year-old German-Swiss administrator was due to "breaches of his fiduciary responsibilities in connection with his employment contract".
"Kattner has been dismissed from his position effective immediately," FIFA said in a statement.
FIFA said it would not comment further on the investigation.
Kattner had replaced Jerome Valcke, who himself was suspended from his FIFA duties earlier this year.