Kattner had been acting general secretary after previous general secretary Jerome Valcke was also dismissed for irregularities.
"Kattner has been dismissed from his position effective immediately," the world body said in a statement.
"FIFA's internal investigation uncovered breaches of his fiduciary responsibilities in connection with his employment."
FIFA said it would not comment further but "will continue its cooperation with the relevant authorities." Kattner, a German, had also been FIFA's longstanding financial director.
The world body named Fatma Samoura as its new general secretary at a congress this month.